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Writer Conflicts with Canon

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When the creator of the work has something to say about said work, the audience often deems their word as something that follows the Canon.
Sometimes, however, it's not the case — what the creator said and what's shown in the work are different.
What could that mean?
If Word of God comes later...
The author might have forgotten about what actually happened in the story.
The author is aiming for a Retcon or Broad Strokes, especially if there's more than one author or if the story writer changes (in which case it's related to Running the Asylum and Armed with Canon).
If the contradicting canonical facts come later...
The author might've changed their mind about what would work for the story (for better or worse).
There's more than one writer, or a new writer replaces the old; in either case they decide to ignore what the God said earlier. Or the holders of the rights to the work disagree with the writer's explanation and tells them to change it (examples of this either qualify as Executive Meddling or Executive Veto). The latter case brings the old debate into discussion: do the license owners determine what's canon and what's not or are the writers the one and only gods?
Or the god has become a Trolling Creator.
This is often why God may opt to be ambiguous instead. Depending on the case, this may lead to Canon Discontinuity or Author's Saving Throw.
Compare with Death of the Author (a belief that the writers have as much of an idea as the audience about the story and thus the writers' interpretation of the story is no more (or less) valid than the audience's), Voodoo Shark (when an explanation just causes more confusion), Flip-Flop of God (when the creator's statements regarding canon are inconsistent or multiple creators have different interpretations on what is canon), Negative Continuity (where it doesn't matter what's canon due to the series lacking a consistent continuity) or Schrödinger's Canon (where a derivative work is somehow both canon and non-canon). This trope often causes a Fan-Disliked Explanation, especially if what the creator says about canon goes against what the fandom has accepted as canon by then.
Please be particular when citing these claims. If second-hand accounts of authorial intent blatantly conflict canon, there's a good chance the author never said that at all.
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Terminator:
James Cameron stated in an interview that Skynet sent the T-1000 back inside a "flesh sac" to get around the "nothing dead will travel through time" rule of time travel. Not only is this a Voodoo Shark which raises the question of why Skynet didn't send anything else like weapons or supplies inside the sac, but it also contradicts every single other piece of Terminator media which comes later — which state that mimetic polyalloy is just good enough to simulate flesh.
Cameron also stated that Skynet sent the T-1000 after realizing that the original Terminator failed in 1984. This contradicts several time travel rules established throughout the franchise, including raising the question of how Skynet would know that a Terminator failed.
And lastly, behind-the-scenes footage shows Cameron telling Arnold Schwarzenegger and Robert Patrick that the battle between the T-800 and T-1000 was the first time that any Terminators had fought each other. This information never appears in the film and contradicts several other sources which state that reprogrammed Terminators fighting for the resistance was a common occurrence — so common that the machines created various ways to counter it.
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When asked about the age of Parian in Worm, writer Wildbow said she was probably 21, because she was midway through her fashion degree after having spent several years working on an engineering degree. In-story, a Stalker with a Crush being the only classmate she spoke to led her to switch out after months. To be fair to Wildbow, when he gave that answer he said he wasn't sure on her age.
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Vampire Knight: One of the main characters, Kaname, is given a flashback with a woman that he's eventually shown kissing. The author came out a while later and said that he only saw the woman as a mother figure, which naturally had many fans raising an eyebrow.
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In the 1990s, when asked, producers involved with The Simpsons would claim Smithers was not generally attracted to men, but just Mr. Burns specifically (the phrase "Burns-sexual" was sometimes used). As the series progressed, this logic was clearly abandoned and Smithers was shown dating and interested in men other than Burns. Although this could be because Burns rejected him in "The Burns Cage" so Smithers decided to pursue other romantic relationships.
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The Kid Flash in Teen Titans: The Judas Contract was stated by James Tucker years after the film's release to actually be Barry Allen rather than Wally West, which is at odds with what was established about Barry's history in the other films of the DC Animated Movie Universe canon, such as no indication whatsoever that this continuity's Barry Allen was ever a member of the Titans and Barry somehow believing Batman to not be real in Justice League: War in spite of being on a team with Robin in his youth.
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Andy Price, one of the main artists for My Little Pony: Friendship Is Magic (IDW), once declared that the comics are fully canon according to Hasbro. However, the comics themselves conflict with the events of the show on a regular basis, with the show going as far as to show explicitly different events than the comics such as a different origin for the sirens and an appearance from King Sombra evil as ever long after a comic gave him a Heel–Face Turn. Jim Miller, the producer of the show, would later clarify that the show paid absolutely no attention to the comics whatsoever and treated them as Expanded Universe at absolute best, explaining why the events of the comics were incompatible with the show despite this claim. The comic writers would eventually declare that the comics were written by Spike to justify this, showing that the comics were unreliable retellings of canonical events, which they were apparently a bit bitter about if this panel is anything to go off of...
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After Thor: The Dark World, both Anthony Hopkins and director Alan Taylor confirmed that the ending was meant to indicate that Odin had been murdered and replaced by Loki offscreen. Odin would later return, alive and well, for Thor: Ragnarok.
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Several things from the Jem Series Bible are ignored in the series itself. For example Clash and Video were supposed to be born on the same day according to the Series Bible, but the series shows that Video was already a toddler when Clash was born.
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Marvel Cinematic Universe:
Kevin Feige has gone out of his way to call the MCU "Earth-616", when that name has been the one for the original comics, with Marvel itself having given the MCU the designation "Earth-199999".
After Thor: The Dark World, both Anthony Hopkins and director Alan Taylor confirmed that the ending was meant to indicate that Odin had been murdered and replaced by Loki offscreen. Odin would later return, alive and well, for Thor: Ragnarok.
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The writer of the first The Lion King: Six New Adventures book has stated that it is a prequel to The Lion King II: Simba's Pride. While fanon has Kopa as Kiara's missing/deceased older brother, canon has yet to acknowledge him. Kiara is Simba and Nala's firstborn according to the sequel and The Lion Guard, though in truth both Kopa and Kiara are Canon Foreigners as Disney doesn't acknowledge direct-to-video sequels or licensed books as canon.
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Rocky Kwaterner: The official backstory for the show as given on the website of Peekaboo Animation is that Rocky became a Human Popsicle for 35000 years when he fell through the ice while trying to take a shortcut across a frozen lake. However, in the episode "The Twist", there's a brief flashback that shows Rocky was frozen because het got buried under an avalanche.
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Steven Universe:
Former supervising director Ian Jones-Quartey stated on Something Awful that "Steven was never 12 onscreen". This contradicts the timeline evident in the actual show, where one summer begins, fall and winter pass, and it's the next summer by Steven's 14th birthday. There were even two annual Beach-a-Paloozas in the meantime.
While on the show's podcast, the co-head writers concluded Lapis did not take all the Earth's oceans in "Ocean Gem", just in the area around Beach City. However, that raises the question of why the surrounding water didn't flow in, and several shots in the episode from space appear to show the planet with no oceans. Granted, the whole scenario is bizarre and highly unrealistic no matter how you cut it.
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Slightly Damned: The race page for Angels claims that they're born like humans. The comic later contradicts this, instead establishing that they hatch from eggs.
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A few years after Gargoyles was canceled, Greg Weisman confirmed that Lexington was gay. In the show itself, he's just as attracted to female gargoyles as the rest of the trio and competed for Angela's affection in Turf. Word of God is that this was because of him being closeted/not consciously aware yet of his orientation, pursuing Angela just because his brothers were, and Greg wasn't allowed to even imply Lex's orientation at all since it went against Disney's Standards and Practices of the time.
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Frozen: After the original movie came out, Word of God was that Kristoff was Sami. Frozen II introduced the Sami-inspired Northuldra, and Kristoff looks nothing like them.
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Don Hahn, one of the producers of The Lion King, said that despite what they say in the movie, Scar and Mufasa aren't biological brothers, since Real Life lion prides with more than two males rarely have them related (which is actually not entirely true). Director Rob Minkoff, meanwhile, claims that Hahn is wrong and Mufasa and Scar are actual biological brothers. Applying Real Life pride dynamics to a setting where lions have a hereditary monarchy is a bit dodgy anyway.
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The information from the Shadaloo Combat Research Institute profiles on the Street Fighter V Character Encyclopedia website raises a number of questions, such as the suggestion that Unknown Soldier Red from Forgotten Worlds is Two P from Final Fight, or that characters from different Street Fighter adaptations and Street Fighter 2010 are in a shared continuity.
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One of the main writers from W.I.T.C.H. has stated that Irma is a lesbian. Even considering this was a Disney cartoon in the mid-2000s, Irma showed not even the vaguest hints of romantic interest in other girls and had male love interests. It's unknown whether he meant that she's bisexual, a strong closet case, or she hasn't realized her sexuality yet.
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Sonic the Hedgehog: Takashi Iizuka's explanation for the lack of humans in certain games, such as Sonic Forces, is due to Sonic and his friends living on a World of Funny Animals. They sometimes world-hop to a human-populated world whenever they wish. This idea, however, muddles up a lot of what was depicted in games released prior to him making that statement. For example, Adventure clearly has Amy living in Station Square (with a NPC even mentioning she has an apartment there), both Knuckles and Tails live nearby Station Square in Adventure, and Shadow's entire backstory was that he was created by humans in Adventure 2. There are no mentions of the characters going between dimensions in-series and multiple games (including Sonic Battle and the two Sonic Adventure games) heavily imply that they live on Earth. The most damning evidence against this is the fact that Adventure (where this "split" allegedly dates back to according to internal documents at Sega) clearly showed Angel Island and Mystic Ruins being in the human world (which also implies that Sonic 3 and Sonic Advance took place there too). The franchise would eventually settle on the idea that anthropomorphic animals and humans just live on separate parts of the Earth (islands and cities, respectively).
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Danny Phantom:
The creator, Butch Hartman, insists that "ghosts" are not deceased people, but creatures from the Ghost Zone that take on the memories and appearances of dead people. While the show does have one throwaway line in this regard, overwhelming in-series evidence establishes that while some ghosts are an example of this, most ghosts really are the deceased humans they depict themselves as.
Hartman has stated that Ember is in her twenties, despite her being called a teenager in her debut episode.
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Final Space:
When asked, series creator Olan Rogers claimed Mooncake to be 5001 years old. However, flashbacks show that Mooncake was created when John Goodspeed closed a breach to Final Space, which can't have been more than 25 to 30 years prior to the events of Season 1 considering John's son Gary, who is 32, was a child when this happened.
On a related note, before Gary was explicitly stated to be 32 in the last episode of Season 2, Olan mentioned that he was 30 years old.
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The various writers of My Little Pony: Friendship Is Magic are happy enough to answer fan questions about the show, but they're pretty upfront about the fact that the show is the only real canon — and anything they say might be overruled by future episodes. In particular, things that Lauren Faust, the creator, say are often ignored by the series as she stopped being involved with it after Season 2. Examples include:
Word of God has stated that, if Nightmare Moon had won in the series premiere, then her eternal night would have resulted in all plants and animals dying. Later, the season 5 finale "The Cutie Re-Mark" shows a Bad Future where Nightmare Moon did win and has ruled for years, but with no negative effect on the environment — or at least what little of it is seen during Twilight's very brief stay there.
According to Faust, the reason for Luna's markedly different season one design, where she's depicted as a young child, was that she lacked most of her magic at the time. She has said it was an on-the-spot explanation and that the writers could explain it some other way. No writer, be it the show or the comics, would bother to try explaining why Luna looked like this after being purified by the Elements of Harmony: the show would never use the design again, even when Luna was drained of magic in a later episode, while the IDW comics would only ever use it when flashing back to Celestia and Luna's childhoods. As an extension of this, Lauren Faust has suggested that Luna is still growing and is physically a teenager; the series itself treats Luna as a full-grown adult.
In season 1, one of the writers stated that all hooved animals were Civilized Animals. The show itself hasn't seemed to take note of this. While the IDW comics featured sapient deer and there were once plans for an episode featuring deer, the show itself ultimately presents them as just another animal, aside from reindeer. Pigs and giraffes are also Nearly Normal Animals as well. The rule seems to be less "all hooved animals, and several mythological creatures, are sapient" and more "all equine and bovine, and several mythological creatures, are sapient".
Faust has stated that, in her opinion, Celestia raised Spike growing up, not Twilight. The episode "Sparkle's Seven" would eventually show that Spike was raised alongside Twilight as her adopted brother.
The official word after Twilight's ascension was that the title of Princess (and the alicornhood it entails) was a merit-based one in Equestria, being granted based on great deeds rather than based on royal blood. This explanation was seemingly abandoned by the introduction of the alicorn-by-birth Princess Flurry Heart, although her existence is treated as an anomaly by characters in-universe.
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Kate Cary has gone on record stating that Dovewing's eyes are blue, and to her, always would be. The sixth arc claims that they're green. Of course, this series has never been very consistent with eye and pelt colors, and Dovewing's eyes have changed colors a number of times beforehand. Plus, her official artwork doesn't help matters. The issue has led to many a Flame War.
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Launch was a recurring character in Dragon Ball, but she didn't appear in the Dragon Ball Z portion of the manga and mainly made a few filler appearances in the early episodes. When asked why, series creator Akira Toriyama claimed to have just forgotten she existed — but there were a handful of lines in the manga indicating that she was written out intentionally; he may have forgotten to bring her back afterward but that's not why she left in the first place.
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It was initially said Identity Crisis was still canon to New 52, despite a lot of it no longer being possible due to the drastic changes that had been made to the DC Universe (such as certain characters no longer existing or having widely different characterizations than they were originally depicted with). Later, in The Button (a Rebirth story), Barry Allen and Bruce Wayne actually witness a scene from it when running through the time stream and don't remember it.
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Aladdin's Forgotten Framing Device was originally planned to end by revealing the merchant was Genie (which was implied by several things, such as them sharing voice actors and uniquely possessing Four-Fingered Hands). The co-directors eventually stated this was still canon, either unaware of or ignoring the end of Aladdin and the King of Thieves, which finally goes back to the merchant and shows him as a character separate from Genie.
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Pokémon: The Series:
Writer Takeshi Shudo claimed that the original intention was for it to take place in an Earth where aliens (Pokémon) have displaced all the animals. This is supported by the Broad Strokes novelization Pocket Monsters: The Animation and by some early Kanto episodes (namely, the Mt. Moon one). Shudo also said that the third movie's plot was originally meant to be about a dinosaur getting revived and no-one knowing what dinosaurs are, because Pokémon have replaced all the animals. Despite this, a number of early Kanto episodes show fish, bugs, and even non-human mammals such as cows, dogs, and other regular animals existing in the anime. Shudo's stance on the matter was that these were errors made by the animators, but regular animals (mostly small ones like insects) have continued to appear occasionally later on.
Word of God is that Misty and Ash are completely platonic. Despite this, they do have Ship Tease even in Japanese episodes. At the minimum, it's implied that Misty likes Ash while Ash, being Ash, is Oblivious to Love.
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The South Park writers had said that they wouldn't allow Cartman to murder anyone. This was after Cartman tricked a farmer into killing Scott Tenorman's parents in "Scott Tenorman Must Die". Cartman would later run over numerous people in "Poor and Stupid" and had Cthulhu kill tons of people in the "Coon vs. Coon and Friends". The "Scott Tenorman" and "Coon and Friends" examples might count under Loophole Abuse, as Cartman does not directly kill anyone, but rather arranges for their deaths.
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Warrior Cats:
Word of God is that Willowpelt and Patchpelt are Graystripe's parents. The problem is that they're full-siblings from different litters. The series occasionally ships distant relatives together but not close ones, especially siblings. It was clearly accidental, in-series they haven't been depicted as mates, and Graystripe's father is unknown.
Several characters have parentages that are confirmed by the writers but aren't mentioned in the text. This leads to oddities with canon, such as Sandstorm not reacting to her father Redtail's death in the first book and no one treating Sandstorm as Ashfur's half-sister through Brindleface.
Kate Cary has gone on record stating that Dovewing's eyes are blue, and to her, always would be. The sixth arc claims that they're green. Of course, this series has never been very consistent with eye and pelt colors, and Dovewing's eyes have changed colors a number of times beforehand. Plus, her official artwork doesn't help matters. The issue has led to many a Flame War.
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This is directly addressed by the creator of Amphibia, who would preemptively state before the release of Marcy's Journal: A Guide to Amphibia that the show and said book override whatever conflicting information he might have said during any prior interview. He uses the ages of the characters as an example, noting that he doesn't even remember saying that Sasha was the oldest.
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Metroid: Series producer Yoshio Sakamoto, on the official Japanese website for Metroid Fusion, answered a number of questions from fans. One player questioned how Samus was able to use the Ice Beam at the end of the game despite it being said her physiology would reject it due to inheriting the Metroids' cold vulnerability, and his response was that absorbing the SA-X restored her previous genetic profile. Metroid Dread retcons this, as not only does she still have her Metroid DNA and cold vulnerability, but it also serves as a major plot point.
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Cullen Bunn wrote Deadpool's Secret Secret Wars and Deadpool: Back in Black — two stories which proved divisive among the fandom, with many complaining about him shoehorning Deadpool into Venom's backstory and insisting that they have to be set in an alternate universe. For his part, Bunn went on record saying they are canon and included references to them in later stories like Poison-X and Deadpool: Assassin. Donny Cates, who took over writing Venom in 2018, went on-record stating that as far as he's concerned Deadpool's Secret Secret Wars and Deadpool: Back in Black are not canon, sparking an argument between the two writers — and even one of Marvel's editors — on Twitter when Cullen Bunn found out.
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Kingdom Hearts: Originally, Tetsuya Nomura stated that Nobodies don't age. Kingdom Hearts: Birth by Sleep shows some of Organization XIII ten years before Kingdom Hearts II. Although they would be Nobodies for nine of the next ten years, they look significantly more than one year younger.
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In YuYu Hakusho Yusuke left for the demon world on what he stated to be his birthday, and that Kurama left 2 months later in July suggesting Yusuke's birthday to be sometime in May. However, Togashi later claimed that Yusuke's birthday was March 26th, making it impossible for Kurama to have left in July as he said.
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Gravity Falls: In the episode commentary for "Boyz Crazy", Alex Hirsch says the show does not take place in any specific year. However, there are numerous in-show details that specifically set it in the summer of 2012 (the year it first started airing). Present-day calendars from episodes such as "Summerween" and "Dipper and Mabel vs. the Future" are that of 2012; and while everything revolving around the Author's disappearance is simply stated to have been "thirty years ago", calendars in locations not touched since the incident (as well as some character dialogue) explicitly place as it happening in 1982.
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A lot of the controversies over Starship Troopers are exacerbated by fans believing that things Robert A. Heinlein subsequently said about the novel's world-building in interviews and essays are contradicted by the actual content of the novel, in particular as to whether any form of public service can qualify you to vote or whether it has to be front-line military service.
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