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  • One Piece:
    • In a mini-arc about Coby and Helmeppo, the two are said to have sailed over Reverse Mountain to Marine Headquarters with Garp. Later on, it is revealed that Marine ships can cross the Calm Belt with special Seastone equipment, and the newspaper photo is hand waved away as a deception for the press.
    • The Warship Island Filler Arc makes two: first when Zoro easily cuts through steel chains, despite it being a plot point in the canon Alabasta arc that he couldn't yet cut steel. Second is that all the Strawhats meet Ryuji, a dragon, which makes Zoro's comment to Ryuma in the Thriller Bark arc that he doesn't believe in dragons seem completely stupid.
      • Later in the manga, the crew meets a dragon for the first time, with all of them expressing surprise as they have never seen one before. Whoops.
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    • At the end of the Warship Island Arc, Nami outright murders the Dragon-in-Chief by knocking him into the sea. Cut to the Dressrosa Arc where Nami considers the idea of tossing a fruit user into the ocean to be too cruel.
    • Another one was when a filler episode had Chopper use two Rumble Balls a short time apart without consequence, when it was later shown taking more than one within six hours has dangerous consequences; taking two should have made him lose control of his transformation. The filler arc was made before that particular weakness was revealed in the manga.
    • At the end of the G-8 Filler Arc it is revealed that Vice-Admiral Jonathan was Admiral Akainu's protegé. At the time the filler arc aired, the manga only revealed the three nicknames of the Admirals, but by that time, Kizaru and Akainu hadn't been introduced yet and nothing about their personalities was known. Jonathan was shown to be a pretty relaxed guy, he respected the Straw Hats, he held no grudge towards them and he's actually glad that they improved the quality of G-8's soldiers and staff members. Akainu is THE General Ripper of the series, is willing to execute deserters right on the stop, he was responsible for the death of many innocent people just to make sure that no criminal was hiding inside the crowd, and he absolutely despises pirates. It's very unlikely that the two of them would ever go along, let alone having a working teacher-student relationship.
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    • In the Impel Down arc, the scene in the control room was extended and added Bon Clay destroying the controls for the Gates of Justice. It wouldn't be big a deal if Blackbeard were not still deep in the prison, which means that Bon Clay's interference should have prevented Blackbeard from escaping the prison and arriving at Marineford.
    • During the Reunion Arc (the first arc to take place after the two-year Time Skip), the anime had Chopper chew a Rumble Ball before transforming into the forms that normally require it, just short of Monster Point. This contradicts a later revelation that, thanks to his two years of training, he now only needs a Rumble Ball for his Monster Point form, and in fact, the original manga scene didn't have him take any Rumble Balls at all.
    • In the Fishman Island Arc, the anime adds a flashback scene of Arlong saving Hody Jones’ childhood Fishman District gang from human slave traders. This contradicts the big reveal of Hody Jones’ reason for hating humans: that he has no reason. He admitted that humans had never done anything to him. The only reason he hated them was because of the racist environment he grew up in.
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    • In Dressrosa, when Doflamingo is about to offer Law a Sadistic Choice at gunpoint, the anime has him address Law by his full name, "Trafalgar D. Water Law". This is despite the fact that Law never told Mingo his full name, only saying that he's a "D" like Luffy...something that Doffy did not even know at all until Law mentioned it. Doflamingo should have had no way of knowing about the "Water" in his name.
  • 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.
    • 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 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.
    • 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 episode 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.
    • 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:
    • The anime tries to explain that 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.
    • Also, 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 makes no sense that people would confuse them.
  • The Dragon Ball franchise was especially prone to this, due to being a tightly plotted series being adapted as the source material was being written. Since Akira Toriyama's Writing by the Seat of Your Pants style meant he didn't bother with giving the anime team notes, and the anime being in a constant state of Overtook the Manga meant they had to create a ton of filler to buy time, it creates a lot of cases where something depicted in the anime directly violates major plot points:
    • In a filler episode of the Dragon Ball animé, Goku meets Dr. Flappe, a professor who lives not far from Jingle Village and was pressured by the Red Ribbon Army into creating Android 8. No such character existed in the manga, which caused some problems when several years later (when the animé became Dragon Ball Z), Dr. Gero is introduced as the creator of the Red Ribbon Androids. Daizenshuu 7 addresses this and notes Flappe might have been Gero's colleague during Android 8's creation.
    • The ship Goku uses to get to Namek is a modified version of the ship he was sent to Earth in, which Piccolo destroyed in a filler episode during the Saiyan Saga. However, the latter issue is no longer present in Dragon Ball Kai.
    • Also in the Dragon Ball Z anime, the line from the manga is cut where Zarbon tells Vegeta that Frieza can transform, leaving a bit of a headscratching moment when Vegeta references it later on. Kai does not fix this.
    • The anime shows Nappa throwing off his armor, which is apparently a massive and heavy object. The Frieza Saga later reveals that the armor is not only very elastic, but also extremely light, so Nappa's armor being heavy makes no sense.
    • Animé filler shows the character Dabura becoming good. Namek's Dragon Balls are then used to wish back the people who are not evil. Dabura should logically have been revived, yet he doesn't appear later as this doesn't happen in the manga.
    • The Garlic Jr. Saga is basically one big adaptation induced plot hole. Neither it, nor any of the movies, occur in the manga. It directly follows the movie Dead Zone, which is supposed to take place before the start of Dragon Ball Z. If Dead Zone was canon, then there's no reason Krillin and the others don't know about Gohan in the first episode of Dragon Ball Z and are surprised when he unleashes his power on Raditz.
    • In the Garlic Jr. saga, Krillin briefly has a girlfriend named Maron, who he ends up dumping by the end. In the eight-year time skip between the Cell saga and the Buu saga, however, Krillin marries Android 18 and has a kid with her with the very similar name of Marron. Although it's not exactly a plot hole per-say, the fact that Krillin would have a daughter with such a similar name to his ex-girlfriend comes across as incredibly odd. Interestingly enough, this actually ended up getting a Lampshade Hanging of sorts in Dragon Ball Super - when Android 17 meets Marron, he mispronounces her name as Maron. 18 promptly gives 17 a Death Glare, and threatens to kill him.
    • In one filler episode of Dragon Ball, Master Roshi tells a story of the creation of the Dragon Balls, which not only contradicts the later canon (which is forgivable because he introduces it as a story he heard, not necessarily claiming it as the truth) but is also out of place because he didn't know what Dragon Balls were in the first place.
    • Similarly, an episode of Z has King Kai tell the story of how the Saiyans were wiped out, and attributes it to the "Kami-sama" of their galaxy summoning a meteor to strike Planet Vegeta in order to rid the galaxy of the Saiyans and their evil ways. As it turns out, this is far from the truth, as Frieza was the one who destroyed the planet, and for less than noble reasons.
    • One of the most egregious examples is the filler scenes after everybody on Namek has been transported to Earth. Vegeta starts acting like a dick, which is typical of him, but behaves in a way completely contradictory of his character motivations. He brags about Goku and Frieza's potential deaths making him the strongest by default, antagonizes the Namekians, and then claims in a flashback during his time working for Frieza that he knew he blew up his home planet all along, even though he was shocked when Dodoria told him this and said he would have revolted if he knew. And then he laughs at Gohan when the news breaks of Goku's "death" and pummels him in a fight before flying off. And then in the next episode he's standing under a tree as if nothing happened, Gohan has no scratches or bruises, and he suggests a method of wishing Goku back to life so he can find out how to become a Super Saiyan and defeat him.
    • Dragon Ball Kai fixes some plotholes (like the Vegeta-dickery from the previous point), but creates some new ones thanks to the fact that it retains some filler while excising others. For example, the Buu Saga retained a scene in Hell where the previous villains watch the final battle on a giant crystal ball. Two of the Oni present recognize Goku as "that fellow who fell off Snake Way a while back", referring to a Saiyan Saga filler episode that didn't make the cut.
    • When Vegeta is about to self-destruct himself to destroy Majin Buu, he asked Piccolo where he would be in the afterlife. Piccolo retorts that since Vegeta has been a ruthless Saiyan for most of his life, he would be sent to hell where he would not only lose his body, but his soul would also be purified until he is reborn without any memories. While it makes sense in the manga as we never saw what Hell looks like at the time, it doesn't explain why many villains such as Frieza, Cell and others in filler, movies and Dragon Ball GT keep their bodies and no-one even lifts a finger in an attempt to purify 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.
    • A variant of this trope is Pantyhose Taro's issue with his name. English-speaking fans usually wonder why he just doesn't use his Embarrassing First Name; this is because Pantyhose Taro's name in Japanese is a singular word (Pansutotaro), and can't be broken up due to how the linguistics work. The separation into "Pantyhose Taro" is a necessarily imperfect translation, as the inherent grammar rules can't be literally translated in English.
  • 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.
  • Dr. 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.
  • 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.
  • Yu-Gi-Oh! had quite a few examples in the anime, particularly with the size of Pegasus's dueling arenas in Duelist Kingdom. It also owes from the anime's Duelist Kingdom arc being something of a Broad Strokes adaptation, trying to carry in as many manga arcs as possible that were necessary to establish the characters without going into great detail.
    • In the manga, Yugi's grandfather was subjected to a nightmarish simulation of monsters attacking him after his duel with Kaiba, something that put him under so much stress that it hospitalized him. As this was cut from the anime, it appeared that he somehow lost a card game so badly that he had a heart attack. This is given a Hand Wave as the holograms and the shock of the torn Blue-Eyes being too much for him, but we see him duel or watch duels quite a few times afterward with no problems.
    • Jonouchi discovering Mai's perfume trick makes less sense in the anime. In the manga, they were sitting relatively close to each other, so it would make sense for Jonouchi to pick up on the scents. In the anime, there's quite a distance between them, not to mention that they're outside, so it should be impossible for Jonouchi to smell the perfume.
    • By a similar token, Mokuba stealing Yugi's Star Chips before he realizes what's going on makes a lot more sense when they're sitting across the table and Mokuba doesn't have to conspicuously run all the way to the other end of a fair-sized arena.
    • In the manga, Kaiba's dueling rings were exclusive to himself and his company, and Pegasus was only able to produce the smaller Battle Boxes, creating a need for him to want Kaiba's technology to make a lifelike, real-size copy of his wife. In the anime, Pegasus's dueling rings were nearly identical to Kaiba's, making one wonder why he needed Kaiba's technology if he already had an equivalent. The dub fixes this by having him need both the technology and the Millennium Items to bring his wife back to life, which he could only get through beating Yugi and acquiring KaibaCorp.
    • Some of the Millennium Items are given one-time-only powers that they never had in the manga, such as the Puzzle being used to swap the souls of Bakura's good and evil sides, though this is phased out post-Duelist Kingdom. That particular power sticks out, given that the resolution to Battle City also involves a villain separating his good side into a different body and holding them hostage, but for some reason Atem decides to do it the hard way this time.
    • In the manga, part of the Battle City ruleset was that most Special Summoned monsters could not attack on the turn they were summoned. This is why Egyptian God Cards are never summoned from the Graveyard for attacks, because since they go to the Graveyard after being revived, they would essentially just sit around for a turn unable to do anything and then die. Winged Dragon of Ra was the exception, possessing an Instant Attack ability that allowed it to attack on the turn it was Special Summoned, which is why it's the only monster where the "dump and revive" strategy was ever used. The anime changed this to only Fusion Summoned monsters having that limitation, which raised the question of why Ra was the only God used in that manner. Furthermore, to maintain its "Instant Attack" ability, they had Marik use Vengeful Bog Spirit in that Duel, which stops monsters from attacking on the turn they were Summoned, and showed Ra bypassing it - and in the process, raising the question of why Ra has an ability that seems to exist just to counter one card.
    • The anime's revelation of the Duel Monster Spirit World in a filler arc (the monsters exist in a parallel dimension that has separated from ours over ten thousand years ago after a war) proved decidedly off when ths manga revealed its own origin (the monsters were created by Egyptian rituals involving the soul during the reign of Atem's father about three thousand years ago). One could say that the existence of the former doesn't necessarily contradict the latter... except for Dark Magician Girl, who was explicitly shown to be the former in one arc (a prominent leader among the Duel Spirits and implied to have been around during the war) and the latter in the other (the apprentice mage Mana's ka spirit and therefore just an extension of her personality and soul). Are they the same person? How did she become independent? Did Mana pull something similar to Mahad? Is Mana some kind of reincarnation? For the most part, the anime just quietly avoids bringing up the Spirit World during that arc and hopes you won't notice rather than furnishing an explanation for how this happened or how these two spiritual arrangements coexist. For even more strangeness, she popped up again for a guest appearance in GX, which featured a Spirit World prominently... only her personality is clearly based on Mana (fun-loving goofy apprentice with a smart side) rather than her character in the filler arc (ancient dignified leader). And she maintains the same voice actress as Mana throughout all of this...
  • 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.
  • Periodically in Sailor Moon:
    • At the end of the first act of the manga, Innocent Bystander Naru is insistent that morning that she and her mother were attacked by "robbers" the previous night (which fits somewhat with the fact that her mother was found taped up and locked in the basement of her jewelry store), who were stopped by Magical Girl Warrior Sailor Moon (she has mercifully forgotten they were a shapeshifting monster). In first episode of The '90s anime, rather than operating under a Weirdness Censor, Naru believes the full incident was All Just a Dream, which raises questions as to whether she remembers that the "dream" monster told her that her mother was Bound and Gagged in the basement.
    • In the Sailor Moon S season, the then-currently condescending Outer Senshi have an oddly polite conversation with Tuxedo Mask (despite him being one of the weakest senshi) and refer to him respectfully as Endymion, despite no other indications that they know much about the existing cast (barring Pluto). This was lifted almost directly from the manga, where the Outer Senshi are implied to already know who most of the senshi are/were but are avoiding working with them out of a sense of duty and penance rather than dislike and skepticism.
    • The anime never explains how Mamoru is able to keep Chibi-Usa alive at the end of Sailor Moon S when her heart crystal is stolen. This is a plot point that is lifted directly from the manga, but by this point the story had already established that he has the power to pass on energy to another person and even heal wounds several times. The anime never establishes him as possessing such a power, but it acts as though he's been able to do this all along.
    • The anime short film Ami's First Love (accompanying the Super S movie) is a straight up adaptation of one of the Exam Battle short stories in the manga, which is about Ami getting a love letter from a secret admirer and freaking out so much she breaks out into hives. The problem? In the anime's timeline, Ami has already had a brief relationship with a Canon Foreigner fellow student, Urawa Ryou (thus this isn't even her first love) and she was shown handling his shy affection for her with grace and maturity. The short film also has the problem of showing Ami using an attack that she only used in the manga without explanation of where she got it. The films already create so many continuity problems that they're generally considered non-canon anyway, but it's still jarring when a story from the manga is adapted straight into a timeline that proceeded so differently as to contradict it.
    • A minor issue is with Uranus being mistaken as a boy. In the original manga, she is intentionally disguising herself as a male student to investigate the Mugen academy. She even poses as a new Tuxedo Kamen in one scene. Sailor Moon only realizes that she is a girl by recognizing her as Sailor Uranus. In the anime, she is simply a tomboy. It never gets explained exactly why Minako and Usagi initially mistake her as a boy, or even why Minako realizes that she is a girl in the end.
      • The same episode where the girls mistake Uranus as a boy also has Neptune deny that they are a couple, even though it was just as obvious.
    • A minor plot hole happens in SuperS in regards to the Amazons Quartet. At the very end of the series, they make a comment about possibly meeting Chibimoon again, and it is also never explained why they're named after goddesses/celestial bodies (a Theme Naming pattern common for the Solar System Sailor Senshi) rather than minerals or metals (a Theme Naming pattern common for the antagonists) — the implication is that they used to live in the asteroid belt, which only raises questions as to their true origins. In the manga, the four of them were actually dormant Sailor Senshi meant to be Chibimoon's guardians, who were forcibly awakened before their time and brainwashed into working for Nehellenia; their names come from the four asteroids that grant them their powers. Because the anime deviated from the manga in handling these characters, and ended up having Chibimoon herself Put on a Bus following the first arc of Stars, this development never happened in this version, leaving the hints that there was more to the Quartet with no outcome.
    • In the Sailor StarS season, many characters remark that Chibi Chibi looks exactly like Usagi. Not just like her little sister, more like her daughter. Well, in the manga, this did make sense as Chibi Chibi is actually Sailor Cosmos, a future form of Sailor Moon herself, and thus they are essentially the same person. In the anime, however, her origin is completely independent of Sailor Moon entirely and it's never explained why they look the same.
    • In episode six of Sailor Moon Crystal Usagi freaks out that she can't transform in front of Tuxedo Mask and reveal she's Sailor Moon, a few minutes after telling him she feels powerless as a leader. She's then surprised to learn he already knows about her secret identity. In the manga, he tells her he knows before she starts worrying about her inadequacies as a Guardian, so her reaction makes perfect sense. (Out of context, her words could be interpreted in a more general sense since she doesn't specifically mention the Sailor Guardians but talking about having to protect everyone while there's clearly a fight going on not too far away doesn't leave much room for interpretation.)
      • Near the end of the same episode, Tuxedo Mask carries an unconscious Sailor Moon to his home so she can rest after overusing her powers. When she subsequently wakes up in Mamoru's room, she is detransformed, with no explanation why this happened. In the manga, she detransforms at will upon waking up, and in general it is shown that simply being unconscious doesn't make a Guardian spontaneously revert to the civilian form, so it's unclear why her transformation was undone in this case.
    • Another episode of Crystal recreated the scene from the manga which reveals that Mamoru survived being stabbed by Sailor Moon because the stones the Shitennou transformed into blocked the blade, preventing him from receiving a fatal wound. In the manga, the possessed Mamoru was explicitly shown carrying the Kunzite stone after the Shitennou's human bodies decayed. In Crystal, however, the Shitennou didn't die until shortly before Mamoru was stabbed, which happened in a different place, so there's no explanation why he had their stones at that moment.
    • Another problem that occurs with the alterations to the Shitennou's plotline is occurs when a brainwashed Mamoru brainwashes Motoki to hold off the Guardians. Any viewer who hasn't read the manga will likely be scratching their heads as to why he doesn't just use the Shitennou, who have been proven to be more than a match for the girls before.
  • 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 haves 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.
  • 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.
  • In the Kaguya-sama: Love Is War anime, Kaguya and Ishigami's tutoring sessions happened in the span of one week before the second semester final exams. 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.

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