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  • Naruto:
    • Naruto claims to have only read 10 pages of Jiraiya's latest novel, Make Out Tactics, in the anime as an extra joke that he was lying when he distracted Kakashi by pretending to spoil the ending. However, later on when he's trying to decode a message Jiraiya left behind while dying, it's revealed that Jiraiya asked him to proofread his books, and he at least obliged to the degree he knows Jiraiya's handwriting well enough to notice that he disguised a "ta" katakana (タ) as a 9. Perhaps he lied about lying he'd read the book, just to annoy Kakashi.
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    • A filler episode expanded Suigetsu and Sasuke's trip to get Zabuza's sword from the Land of Wave, and it's mentioned that Inari and Tazuna would be working on a job in the Cloud Village for the next year. However, in the manga they actually ended up making guest reappearances in a job in the Leaf Village (helping rebuild after the Pain invasion) what was at most a couple of months later.
    • A smaller one is how the anime gives the Fireball Jutsu to various characters that aren't members of the Uchiha clan or who are officially unable to perform Fire techniques.
    • During Itachi's fight against Naruto and Kakashi in Shippuden, it is stated that Itachi's Sharingan is not affected by the Hidden Mist technique. This contradicts what happened in the Land of Waves arc, where Kakashi's Sharingan was rendered useless against Zabuza's technique.
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    • Omake should probably not be considered canon in general, but an early Shippuden omake has a really noticeable one where Deidara casually asks Kisame what Itachi is like as if he's never met him, even though Deidara was (forcibly) recruited into Akatsuki by Itachi in the first place and Deidara had spent the last several years trying to find a way to kill Itachi.
    • One Filler arc had Hinata learn a unique, powerful technique featuring myriad pinpoint-precision chakra laser beams. Later in the manga, a major villain is able to curb stomp her using his powerful gravity blast attack—she spends the fight repeatedly charging at him while trying to land a physical hit, which is hopeless. The chakra lasers would have obviously been a much better bet.
    • The above-mentioned arc also has a glaring issue with the villains being stated as grandchildren of the First Tsuchikage, WAY before he actually debuts in the manga in a flashback of the Third and current Tsuchikage's. Why is this an issue? It is because the Third is the First's grandchild in that continuity and the latter is already a 79-year-old man by the time he first appears whereas the grandchildren from the filler can't be any older than 30-something at best. The same arc also says that the original Tsuchikage was an insect user like them but nothing the actual man shows in the flashback in either media remotely hints at such.
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    • In the anime Obito is able to suck Fu into his Pocket Dimension without touching him, while in the manga it was not clear if he touched him or not and it was later explicitly stated to require physical contact, which was exactly why Minato was able to beat him.
  • Death Note:
    • The anime adaptation omitted several scenes from the manga, which while usually not problematic, have led to plotholes. In the manga, it's explained that SPK member Ill Ratt is actually a spy for Mello, which is how the mafia learned the SPK's names and were able to kill them. This is not explained in the anime, but in the Relight 2 special, the mafia are cut, and Light blackmails the president to send their names to Kiyomi Takada. In this version, Light's meetings with her and Teru Mikami are moved to earlier than occurred in the anime, and they kill the SPK.
    • However, while fixing one plothole, said special creates another: as the mafia are cut, Soichiro making the trade for Shinigami Eyes and subsequent death is omitted in the process, leaving plotholes regarding Soichiro's absence as well as how Light was able to acquire Mello's true name.
    • Also in Relight, they have one scene where Light says to Ryuk that talking with him would be impossible due to his room being bugged by L, but two scenes later they are shown freely talking without any mention of said cameras being removed.
  • Bleach:
    • In both anime and manga, when Ichigo first meets Renji, Renji expresses surprise over the size of Ichigo's zanpakutou. Ichigo admits he noticed it was large compared to Rukia's but, not having met any other Shinigami until now, he had nothing to compare it to. The anime creates the plot hole because it had inserted Ship Tease scenes in Episodes 8-9 where Ichigo fights another Shinigami over Rukia and therefore gets to see another Shinigami's weapon up close. These scenes do not exist in the manga.
    • When the anime covers Chad's backstory, it bizarrely changes the manga story. In the manga, Chad's grandfather lectured him against being a bully so Chad obeyed his grandfather and vowed to never fight for himself. Ichigo realised Chad could fight for others so the two vowed to fight to protect the other; Chad therefore only ever fights to protect others. In the anime, Chad ignores his grandfather until his grandfather is beaten almost to death by Chad's victims. Horrified, Chad vows never to fight again. Since the anime has Chad fighting to protect others, just as the manga set him up to do, Chad's anime behaviour completely contradicts the anime version of his vow.
  • In Yu Yu Hakusho, the group uses Yanagisawa's Copy power to copy Kaito and use his video game skills to win a round against the Game Master. In the anime, the group uses Yusuke (who is otherwise not very good at video games) to win a fighting game, which makes their desperation to win when Kurama comes up seem strange; in the manga, only Yusuke and the non-gamer Hiei were left, but in the anime, they could have utilized Yanagisawa's power.
  • In the Fist of the North Star TV series, during an episode where Jagi terrorizes a village while pretending to be Kenshiro, one of the villagers remarks that Kenshiro was the one who defeated "Devil's Rebirth and the Fang Clan". However, not many people outside Jackal and his gang were even aware of Devil's existence. In the original manga, the villager simply said that Kenshiro defeated Jackal instead. This change was likely done due to the fact that Jackal was an independent villain in the manga, whereas in the TV series he was simply a lackey of Shin.
  • Code Geass: In the final volume of the manga, the removal of some characters and plotlines led to several Out Of Character Moments. For example, Kaguya, who is Zero's biggest fangirl, not to mention absent during the meeting, is essentially the engineer behind the Black Knights' coup d'état against him and the one who smooths things over after he escapes; in effect, she takes up the roles of Diethard (who isn't in the manga) and Ohgi (whose motivation to betray Zero came from Viletta's excised storyline).
  • Inuyasha:
    • In a few early episodes of the anime, shikon shards are needed for Kagome and Inuyasha to travel through the well. This was never the case in the manga, and Kagome spends quite a while without any at all but still travels through the well, so it stops being a requirement in the anime without explanation.
    • Many plot points center around Kagome and Kikyo looking alike (Kagome being Kikyo's reincarnation). In the anime, nearly everything about them looks different—-eye shape; hair color, texture, style, and length; skin tone; and even height—-so it makes no sense that people would confuse them.
  • Plot Holes seriously tarnish what is an otherwise excellent series in Flights of Fancy, the second season of the Ah! My Goddess TV series— Skuld is seen using her stamp power in one late episode, but there's no episode in which we see it developed, and Chihiro, and her shop, Whirl Wind, show up, but Chihiro is never formally introduced, and the fact that she wanted to start a shop is never even mentioned.
    • Flights of Fancy also inverts this Trope: Keiichi and Belldandy are an Official Couple by Episode 24 of Ah! My Goddess; at the end of the Lord of Terror arc, they share a moment together when they confess their love for each other. In the 24th (and last) episode of Flights of Fancy, Keiichi spends the entire episode trying to confess his love for Belldandy, but Cannot Spit It Out— even though Belldandy flat-out says she's ready for him to say it!
  • Hellsing: In his fight with Alucard, Luke Valentine is shown to have a strong Healing Factor, surviving after getting shot in the head by Alucard's specialized gun. However he is unable to regenerate his legs. In the manga there was no headshot. He was instead shot in the stomach by the Casull, while his legs were shot off by Jackal. In the OVA, Jackal was the cause of all three wounds. This was rectified in the Blu-ray re-release, where Luke's initial injuries are now caused by the Casull.
  • In Ranma ½, Ranma (as a girl) competes with Tsubasa (whose disguise had yet to be revealed) in who can sell more food to the boys at school, but since all of them knew that Ranma wasn't a real girl they didn't buy any from her until she started wearing a disguise. However, in the anime Ranma's curse wasn't revealed by this point, so the boys bought them only from the disguised Ranma for no apparent reason.
  • Saint Seiya had one when they showed Scorpio Milo killing Shun's Master. Then the manga came out and it was Pisces Aphrodite. A number of Ass Pulls had to be done to fix the problem of Shun swearing revenge against someone who didn't apply the coup de grace against his teacher.
  • The final season of the Shakugan no Shana anime has a pretty massive one surrounding Yuji's Face–Heel Turn in becoming the avatar of the Snake of the Festival and the leader of Bal Masque. It comes completely out of left-field, as the show skips several important character moments and plot points from the novels, not the least of which include Yuji meeting and being tempted by the Snake of the Festival, and the development of his increased aggression and well-intentioned extremism.
  • Doctor Slump had a story where Akane dressed up as Miss Yamabuki to play some pranks on Senbei. This took advantage of their faces looking the same. The second anime made their faces more different (And gave them different hair colors), yet they adapted this story even though it didn't make sense any more.
  • Berserk (1997) ends with Guts facing certain doom, but then skips to him still alive in The Stinger (looking as he did in the Action Prologue). As Skull Knight, the guy who saved him in the manga, was Adapted Out, this just seems blatantly nonsensical.
  • Berserk (2016)'s main plot kicks off with Guts being subdued and captured by the Holy Iron Chain Knights, who don't seem to inflict that much damage to him and are noted in-story to be mostly incompetent Lord Error-Prone types (with the exception of Azan, who puts up a pretty good fight but doesn't do much lasting damage). This is rather jarring, as the rest of the series depicts him as a demon-slaying One-Man Army with Charles Atlas Superpower who would treat the Knights as little more than a speedbump. The difference was that in the manga, Guts's encounter with them happened immediately after his fight with the powerful Apostle Rosine in the Lost Children arc, which was a knock-down drag-out brawl that involved him being Impaled with Extreme Prejudice, getting set on fire, and eventually falling several stories, and to add insult to injury, when the fight was done, he got shot with a crossbow by a supporting player in the arc. So not only was he basically on his last legs, but it meant that Combat Pragmatist Serpico was able to disable him by targeting his wounds with a hunk of wood. The anime cut out the Lost Children arc entirely, its story kicking into gear when Guts meets the Knights, so to the viewer, it seems like Guts made an utterly embarrassing showing—especially since now Serpico's thrown hunk of wood is targeting a wound that isn't there.
  • Elfen Lied:
    • The anime begins with a violent demonstration of Lucy's immunity to bullets, despite the fact that the guards are supposed to have special bullets designed to penetrate her vectors. In the manga, she grabs a Human Shield before any of the heavily armed guards can get a shot off.
    • The anime also gave Lucy only four vectors, as opposed to the seemingly unlimited number she had in the original, while allowing her to do things she did in the manga that would be impossible with only four vectors, such as simultaneously holding a few hundred bullets in mid-air.
  • The anime adaptation of the video game Tales of the Abyss suffers from its Compressed Adaptation status. Sometimes it's only Adaptation Explanation Extrications, but other times are full blown plot holes. The most obvious example is Ion's death, which it's explained in the game, but in the anime comes practically out of nowhere and without any tangible reason.
  • Fullmetal Alchemist:
    • Brotherhood has a pretty noticeable plothole. Roughly about 2/5ths through the manga, all hell breaks loose and sees Alphonse, Mustang's group, Barry the Chopper, and Ling and Lan Fan get caught up in a battle with the Homunculi. Ling and Lan Fan fight Gluttony and Ling manages to cut Gluttony in half. Gluttony immediately heals up from this, which causes Ling and Lan Fan to learn about the Homunculi's regenerative abilities. When Ed returns from Xerxes later on and reveals his plan to capture a Homunculus, Ling and Lan Fan want to get in on the action because of their knowledge of the Homunculi's regeneration since it relates to their own quest to find immortality. In Brotherhood, the two's fight with Gluttony is completely cut, but they still want to join on Ed and Al's plan to capture a Homunculus for the same reasons, making one wonder how they know about the Homunculi and their power to regenerate. This is fixed by the dub, as Ling overhears Ed mentioning that Homonculi are immortal.
    • Another example from Brotherhood happens due to the anime condensing the early chapters of the manga in order to reach new material that the first anime hadn't adapted. It was shown that, after Ed's first battle with Scar, Lust is tailing him on the same train to Resembool in order to protect him in case Scar returns. Thus when Armstrong calls out to Dr. Marcoh, whom he recognises at one of their pit stops, Lust ends up seeing the Doctor as well explaining how she was able to track him. In the anime there is no indication that Lust in following Edward so it seems as if she just arbitrarily finds the Doctor right after Ed, Al and Armstrong do.
    • In the first anime, Greed's plan to bind his soul to an inanimate object was a failure before it even began, since homunculi in the first series had no souls to begin with. He was aware he had no soul, too.
  • The first episodes of Detective Conan anime removed several references to Dark Organization and its members that existed in the manga, causing two examples of this trope:
    • In Shinkansen Bomb case (animated as episode 4), originally it was the Those Two Bad Guys who gave Shinichi that fateful Fountain of Youth that planted a bomb on the train, and during the case Conan (i.e. the alias Shinichi took after being shrunk) overheard their code names: Gin and Vodka. In the anime the criminals were no longer members members of Dark Organization but some random criminals, so this left a plot hole in the anime that was never adequately resolved— when these names were needed in the third season, Conan just mentioned that without any explanation on how he knew that in the first place.
    • The Billion-yen Robbery Case involves the death of Akemi Miyano, a Dark Organization mook, in the hands of the same Gin and Vodka. In the anime (Episode 12), the Dark Organization aspects of this case were completely removed— the said mook did not die, and she wasn't injured by Gin and Vodka either. This caused a case of Schrödinger's Cast as the said mook's death under the hands of the Dark Organization is essential to the plot, and she became the focal point of many, many backstories. An anime original episode was thus made right before one of those important backstories unravel, where the said mook was killed by Gin.
  • Little Busters!: In the Visual Novel, Kud's reluctance to return to Tevua stemmed partially from her relationship with Riki and partially from her fear of the dangerous conditions there, and only lasted for a couple of scenes. The anime drew this out, instead using this plot point to show Kud's backstory and how she felt unable to become a cosmonaut like her mother and was ashamed of herself, and claiming that she came to Japan to 'escape' from this. Nicely dramatic...but then why does Kud speak fluent Japanese? In the visual novel, it's made clear that Kud was always meant to go to high school in Japan and so had been taught Japanese as her dual first language with Russian. But in the anime, her moving to Japan was treated as a sudden whim outside of her mother's knowledge.
  • A few exist in Robotech thanks to its origins as a Cut-and-Paste Translation:
    • Why does Dana Sterling have green hair as a baby but is a blonde by the time she grows up? Dye job? Or because she was originally two different characters (Komilia Maria Fallyna Jenius in Super Dimension Fortress Macross and Jeanne Francaix in Super Dimension Cavalry Southern Cross)?
    • Why, when humanity come across Zor Prime, do they act surprised when they analyze him and find out he's basically human (never mind the shoehorned-in "and not just a micronized Zentraedi" statement pointing out their alleged familiarity with Human Aliens - surely the races are so similar as to be practically the same species, as they can interbreed)? Maybe the fact that the original Super Dimension Cavalry Southern Cross character actually was a (brainwashed) human, Seifriet Weisse.
    • Why cities such as New York (complete with famous Real Life theatres) exist in The New Generation series when the Earth got nuked by the Zentraedi and they barely managed to rebuild before being invaded again by the Invid? Maybe because there were no Zentraedi in Genesis Climber MOSPEADA to begin with.
  • In the manga adaptation of Puella Magi Madoka Magica, due to its nature, they had to cut out some scenes from the final stretch of the anime. One of those scenes was a Meaningful Funeral, which had its purpose be that Sayaka's body, which was left in the apartment by Kyouko, was found. Cutting out that scene just suggests that the corpse is still rotting in the apartment.
  • Shinji's reluctance to pilot the Eva in the Rebuild of Evangelion series makes far, far less sense than in the original Neon Genesis Evangelion, in which he made sure to ask what would happen if he were gone, and Misato assured him Rei would replace him. In 1.0, she egged him into leaving despite knowing full well the fate of humanity rests on his shoulders, and in 1.11, he realizes only seconds before starting the final decisive battle of the film that other people’s lives depend on him, despite having seen what an Angel can do.
  • The anime of Umineko: When They Cry contains so many of these (either by misinterpreting scenes from the visual novel, going for Rule of Cool or because of Compressed Adaptation) that the mystery becomes impossible to solve on one's own:
    • The first two are in episode 5 alone, where Battler shoots a bullet at the portrait even though the gun he picked up is supposed to be unloaded and sees gold butterflies (while in the VN Beatrice appears in person) which are supposed to indicate we are watching a fantasy scene. So the detective shouldn't see them, the only exception being the end of Episode 2, where Battler had surrendered.
    • Another one is in episode 10, where Shannon's corpse is found with the stake in her forehead; while in the VN the fact that the stake is beside her corpse is an important clue that she committed suicide in Episode 2 and 4.
    • Yet another is how in the anime, Shannon and Kanon would appear together in front of other people, such as the cousins, in scenes that weren't fantasy. In the visual novel, the fact that Shannon and Kanon never appear together in front of the other members of the family outside fantasy scenes is meant to be foreshadowing for how they're actually one and the same.
    • And of course, the entire first half of the Episode 4 Tea Party is axed, along with several important bits of information.
  • BlazBlue: Alter Memory has Ragna leave a nearly dead Hazama alive to go find Rachel and Noel. While the game establishes this by saying that Hazama has a lifelink active (which requires one to kill both members of the lifelink at the same time in order to have them die), the anime doesn't bother stating it and makes Ragna look like an idiot.
  • In I Can't Understand What My Husband Is Saying, one of the main characters is shown to be a smoker in the manga, but not the anime. This becomes a problem when she's told that she needs to quit in episode 6.
  • At the end of the Gunslinger Girl anime Angelica dies. This is all perfectly fine since it's the last episode, but four years later they created a new anime called Gunslinger Girl Il Teatrino. It's closer to the manga and Angelica was revived, as she doesn't die until halfway through the manga. The problem is Teatrino tries to act as a sequel to the first anime, and her falling asleep instead of dying ruins the impact of the original ending.
  • The first episode of Wandering Son has Yuki buying Takatsuki a gakuran. In the manga Takatsuki already has a gakuran. He wore a gakuran frequently while out as a boy. The gakuran is even a hand-me-down from his brother.
  • In Ooku The Inner Chambers, the shogunate bypasses the closest heir, Tokugawa Harusada, in favor of her son Toyochiyo (Shogun Ienari). In real life, the reason Ienari became shogun was because he had been adopted by his predecessor Ieharu to become his heir. In Ooku, though, no such adoption ever took place, and everyone had expected Harusada to become the next shogun, making her abdication one of these, especially since no explanation's been given so far as to why she turned it down.
  • The Sick Episode from Monthly Girls' Nozaki-kun revolves around Sakura, Hori, and Waka having to guess how Mamiko, the heroine in Nozaki's manga, would act after Nozaki gets sick and is unable finish his current chapter. They never even think to call their friend Mikoshiba for help, despite the fact that Mamiko's personality is explicitly said to be based off his, meaning he would likely have some insight into how to write her. The manga chapter this episode was adapted from contained a line stating that they would be unable to reach Mikoshiba since he was either buying or playing a newly-released Dating Sim, but for some reason this scene was omitted from the anime.
  • A large amount occur in the anime adaptation of Tokyo Ghoul, due its severely compressed nature. One of the more notable ones is with Tsukiyama. In the manga, Tsukiyama becomes a major ally of Kaneki's in the latter half and goes through significant Character Development, culminating in a confrontation with Kaneki where he attempts to prevent Kaneki from going on a suicide mission, which causes Tsukiyama to eventually have a mental breakdown. In the anime, the plot is altered so his Character Development doesn't happen, but the confrontation plays out pretty much the exact same way, which makes his reaction come off as completely overblown and random, considering he and Kaneki have barely got know each other. Another example is that in the manga, it is revealed that Dr Kanou was intentionally creating One-Eyed-Ghouls for Aogiri and Kaneki was a successful experiment. This (along with Kanou's character) is cut from the anime, so the existence of the twins Kurona and Nashiro go completely unexplained.
  • The anime of Karneval drops a sub-plot early in the story in which Nai is framed for murdering a policeman, leaving it unexplained why Gareki needs to keep him hidden from the police in subsequent scenes.
  • Attack on Titan:
    • In the anime, the Titan eating Eren's mother is shown intentionally breaking her spine beforehand, which makes little sense for a mindless Titan to do. Though Eren's mother was struggling against the Titan's hold, it's possible the Titan was at least smart enough to know that crushing her would make her stop squirming.
    • Episode 25 shows Levi, getting Eren out of his Titan form in his 3D Maneuver Gear after defeating Annie, despite that he had an injured leg back in Episode 22, which was emphasized several times. In the manga, he wasn't able to participate in capturing Annie because of his injury.
    • In the manga, titan!Annie was scaling the Wall so quickly that titan!Eren had to throw Mikasa in order to reach her. In the anime, Mikasa was somehow able to reach her all on her own (though it would appear that titan!Annie was climbing the Wall much slower than in the manga).
  • Fairy Tail: While the anime will often make little corrections to Mashima's consistency errors, coming close to the manga has caused it to create a few of its own. The shadowy figure that Jellal is kept from pursuing is changed from a spiky haired silhouette to the hooded girl, for instance. While that was generally assumed to have been Mashima not knowing how the figure should look until later, a manga chapter that came out at almost exactly the same time as the episode revealed that it actually had been Future Rogue, not Future Lucy.
    • The anime also had the Trinity Raven guild escape the Tower of Heaven before it collapsed, whereas they are implied to die in it in the manga. Along comes chapter 482 and 483, and it's revealed that they actually did die in the Tower, since a villain uses a spell that conjures dead people, and Ikaruga is one of them.
  • While Gintama is mostly consistent (helped by two breaks), it suffered this when The Movie included a flashback scene that strongly implied that Gintoki was taken in later by Shouyo after Takasugi and Katsura, only for it to be established later on that it was the other way around. Unsurprisingly, when the anime finally adapted those chapters, it lampshaded the problem two episodes later were Gintoki answered fanmail and promptly made up a deliberately nonsense explanation.
  • The Legend of Zelda: Ocarina of Time:
    • The manga adaptation of The Legend of Zelda: Ocarina of Time skips the Temple of Shadows, meaning that we see Link collecting only five medallions... but when he has to break the barrier around Hyrule Castle, the sixth medallion appears out of nowhere, along with Impa in the group shot with the other sages.
    • The manga has a lot of foreshadowing for Sheik being Zelda in disguise. Even before Zelda is formally introduced, Link meets her in disguise playing outside town (which foreshadows her being a Tomboy Princess). Later on we have more clues such as Sheik being light to hold and Sheik covering his chest after he awakens near Link. While it's technically true that Sheik being Zelda is kept, Impa put Zelda in essentially a magical coma. Sheik is a male personality, not Zelda actively pretending to be male. This ruins the former foreshadowing and adds an element of Adaptational Wimp to Zelda's character. To make it more confusing, the manga also otherwise treats Zelda as if she was in control the whole time.
  • The first episode to Your Lie in April has Kousei mention that he has brown eyes. This is despite him very clearly having blue eyes.
  • Ace Attorney: A major part of Phoenix's backstory involves "class trial" when he was accused of stealing lunch money. Phoenix was sick the day the money was stolen and didn't attend PE class, so when he was the only student without an alibi, everyone assumed it was him. The anime-only episode "Turnabout Promise" extended the scene by showing Phoenix taking the envelope the money was in, and being seen by a girl from his class. However, despite being seemingly caught red-handed, the trial goes the same way it did in the game with Edgeworth claiming they accused him with no evidence. The fact that Phoenix was seen by someone isn't brought up at all.
  • In Magical Girl Lyrical Nanoha A's, Chrono's staff Durandal was created by Gil Graham to fight the Book of Darkness. Due to Graham being Adapted Out, the movie changed it to originally belonging to his father. All well and good, were it not for the fact that Chrono's father died via exploding spaceship while on duty (meaning he would have had his weapon with him), which makes you wonder how in the hell Lindy got a hold of it.
  • Full Metal Panic! has a small version of this: Gauron's twin assassins mistakenly pronounce Kaname's surname Chidori using the Chinese reading of the characters. This makes sense in the original light novels and the anime adaptation, where they're Chinese; it's less logical in the manga adaptation Full Metal Panic! Sigma, which makes them ambiguously Caucasian Gothic Lolitas.
  • City Hunter: In few filler episodes of the anime main character Ryo gets on a plane or helipcoter. After in the manga, it is revealed that Ryo's afraid of flying.
  • Miss Kobayashi's Dragon Maid:
    • Due to the chapters being adapted out of order, Lucoa and Fafnir checking up on Tohru during the dodgeball chapter loses most of its meaning. In the manga, it happened right after the whole debacle with Tohru's father, but it happened beforehand in the anime.
    • Due to the change of how Kanna gets her hands on the chocolate that Tohru made, the anime adaptation of the Valentine's Day chapter leaves out the crucial plot point of how the Love Potion had no effect when consumed by a dragon (in the manga, Kobayashi is unaware of this, and ends up eating some of the chocolate when offered by Kanna because she assumed that if Kanna's eating it without any odd effects, it would be safe for her to eat as well).
  • In the anime adaption of the arc from Snow White with the Red Hair, in which Zen, Obi, Kiki, Mitsuhide and the Mountain's Lions rescue Shirayuki and Kazuki the pirates base is discovered after Raji chases the pirates in an attempt at giving the unapologetic attempted rapist Adaptational Heroism. Unfortunately this means that Zen not only allowed Shirayuki to be taken out of his sight to be sold into slavery at an undisclosed location it also means he conscripted Kiki to the same fate. In the manga the entire plan was generated because they already knew the location of the pirate's hidden base and were forcing them to return there in order to ambush them.
  • In the seventh Kara no Kyoukai movie, when Shiki takes Kokutou home from the hospital, they walk under the blooming Cherry Blossoms to emphasize their newfound romantic happiness. This was changed from the original novel, where the scene takes place against the backdrop of appropriately severe early-March weather, and becomes a plot hole when the epilogue rolls around, taking place the day after Kokutou leaves the hospital, and Mifune City is in the throes of heavy snowfall again (which is actually foreshadowed by a weather report in the original novel). While not a major plot hole by any measure, it is obvious that the director of the adaptation has sacrificed internal consistency for the romantic spectacle in this case.
  • The light novel of Gosick establishes the Grey Wolves are supernaturally unable to leave the Old World and will die of illness if tried. That's the true reason why the last Brian Roscoe dies in the ship and why Victorique's hair turns silver; she only manages to survive the ordeal because she's technically only a half-Grey Wolf. However, in the anime continuity Roscoe is another half-Grey Wolf himself, which means he should have survived with just decolored hair just as Victorique if the rule still applied. The reason why he suddenly dies in the ship, even although he seemed to be only superficially wounded and was receiving medical attention, is never explained, nor is Victorique's hair change. If anything, it's only implied that it might be a case of Death by Despair and Prematurely Grey-Haired respectively due to all the tragic events.
  • Sonic X:
    • Eggman has a realization that he was born on Earth, but this ended up never being elaborated on. It's unknown how Eggman ended up on Sonic's World and why he has no memory of his past on Earth. In Sonic Adventure 2, Sonic and his peers live on Earth amongst humans.
    • The anime follows Shadow's backstory from Adventure 2 to a T but never explains how (or why) humans from Earth created a Funny Animal and why this Funny Animal just so happens to look like Sonic's kind. In the games this is explained by Funny Animals and humans coexisting.
  • Kaguya-sama: Love Is War:
    • Kaguya and Ishigami's first tutoring sessions happened in the span of one week before the second semester final exams in the anime. However, they still kept the "Ishigami plays games right before the exams" gag, despite the fact that Kaguya would never allow it while he was under her tutelage. This plot hole doesn't exist in the manga, where the tutoring sessions were for a later test.
    • Hayasaka is shown looking at a series of photos on a tablet while scolding Kaguya for her lack of progress with Shirogane in episode 16, the last of which is from the moon viewing. While that picture does exist in the manga (having shown up when the Student Council put all their photos into a group album at the end of the Cell Phone arc), it's unclear how she got her hands on it given that Ishigami was presumably the one who took it and it's unlikely he would have shared it on social media for fear of Kaguya's wrath.
  • The Quintessential Quintuplets:
    • In the manga, the titular identical quintuplets can only be told apart from each other by their hairstyles and manner of dress, resulting in quite a few situations where they impersonate each other, either comedically or seriously. While the color spreads make their hair out to be a shade or so lighter or darker than one another, the anime bumps this up to outright different colors, and further differentiates them through distinct voice actresses. This makes any situation where one of the girls fools someone into believing she is a different one of her sisters look less like cleverness on her behalf and more like a case of the opposite party grabbing the Idiot Ball, since to the viewer it's blatantly obvious which of the sisters is which.
    • The flashback photo of the quintuplets as children brings up another point of discontinuity—in the manga, it's in black and white, but since the girls are all shown to have the same hair color it's reasonable to assume that they also did in the past. The anime also shows that all the girls as children had the same hair color, but in this case they have different colors as teenagers and the hair color they had as children is shown to be different from any of their current ones. Unless every single one of the quintuplets in the anime is hair dying, it just comes off as a bizarre continuity error.
  • In the Sound! Euphonium novel, the characters speak with Kansai dialects. This dialect is absent in the anime adaptation. This causes some issues, such as Reina and Kumiko's Platonic Declaration of Love coming off as less ironic.
  • Several episodes of the Pokémon anime have aspects that contradict the games. One of the most notable instances of this is the episode "Showdown in Dark City," where Electabuzz and Scyther are revealed to hate the color red. However, Scyther would later receive an evolution, Scizor, with a red body, which would imply it hates its own evolution. Another episode, "Pokemon Shipwreck," has Meowth try to eat a Magikarp, only to be met with hard scales and Misty claiming it's just scales and bones with little edible material. This makes little sense in the context of Pokedex entries mentioning Pidgeot hunting Magikarp, and comes off as plot convenience more than anything else.
  • The Tower of God anime has some mild ones where characters end up behaving implausibly.
    • Baam's Die or Fly moment at the end of the Crown Game is much more dramatic in the anime, and lots of people see him explode into a huge column of Shinsu... so it's incongruous that none of the other Regulars afterwards treat him as the guy who did something totally amazing. Even when Hoh is talking about how weirdly talented he is, he never brings that one up. In the original, the Shinsu just slashes at his opponent, and it makes sense that only Lero Ro understands something very out of the ordinary has occurred.
    • In the Hide and Seek test, it's shown that Quant has enough Super Speed to just whoosh past any Regular (even Anaak) before they notice, and he can also freeze someone with Shinsu while doing so. So it's kind of weird he doesn't do anything about Hoh holding Rachel hostage, even when Hoh is distracted, especially when Quant is really angry about it at first but then just decides to leave. The English dub (which is often missing the point slightly) even has Quant bring up the possibility of freezing Hoh before turning to leave without doing it. In the original, Hoh and Rachel are within the safe zone Quant can't enter because he's their opponent in the game, but that doesn't exist in the anime.

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