Cross Marian of D.Gray-Man, who was more a Jerk with a Heart of Gold in the manga. The anime seemed to lean on making him a complete Jerk Ass. His treatment of Allen. The anime has Cross asking Allen to bring him lions, selling him into slave labor, and at one point, pinning him to a wall to take his money. The scene reminiscent of a pimp and prostitute, including Allen asking Cross how long he's going to be forced to make money for him. Also, the latter scene happened while Cross was living in a palace with a Maharajah's widow. Thus, he wasn't in dire need of money at that point. Manga-wise, Allen said he gambled if they really needed money. None of the aforementioned scenes happened, or were hinted.
There's also the scene where guards drag Allen away from Cross in HQ, and Cross waves him off, while smirking and humming. In the manga, the latter things with Cross didn't happen. All Cross does is watch, thinking it was quick.
Then also, in episode 27, Cross is said to have taken money from a woman when her boyfriend came after him. He is shown being a lover to a rich widow, and Allen states Cross has a thing for rich women. In the character fanbook, written by Hoshino Katsura, Cross is stated as liking "good" women. So the anime makes Cross look like a gold-digger, who specifically looks to take / use women's money.
To a lesser extent, King Dedede of Kirby of the Stars (pictured). While still rarely exceeding a petty comedic Jerkass, his anime counterpart has far fewer benevolent moments than that of the original games and usually plays the main antagonist of each episode. In the games, Dedede is more greedy and selfish than outright evil - when Kirby is up against a truly dangerous villain like Zero or Nightmare, Dedede usually ends up joining forces with him to defeat it, and sometimes (such as in Kirby's Return to Dream Land) genuinely tries to help Kirby out and acts in defense of Dream Land. In Kirby: Triple Deluxe, he even saves Kirby from Sectoria with no prompting. Even when he's an antagonist, he's more often than not misguided or brainwashed. For his part, especially in the more recent games, Kirby seems to view Dedede as a friend.
Some of the Gym Leaders and Elite Four members. While most of them (with the exception of Giovanni and Malva) are good guys in the games - Lance and Lorelei even helping out the player character at key points - Lt. Surge, Koga, Sabrina, Agatha, Bruno, Lorelei, Lance, Karen, Will and Pryce became villains in the manga adaptation Pokémon Adventures. To be fair, though, Pryce is a more sympathetic Anti-Villain, Lance is a Well-Intentioned Extremist, and most of the other characters listed reform later on, with the exception of Agatha.
This is utilized to a lesser extent with their anime counterparts. Creepy Good Sabrina is converted into something of a demonic witch who antagonizes Ash and co., while many others, most notably Lt. Surge, Erika, and Skyla, are egotistical Jerkasses with a condescending demeanor towards their challengers (or, in Erika's case, towards those who don't appreciate the perfume her gym makes). Pryce is a Jerk with a Heart of Gold who is cold towards Pokémon due to a misunderstanding with his Piloswine long ago, although he does get better when the Piloswine is found and the situation explained. In particular, Sabrina in the games is implied to be a good-natured person who happens to have frightening powers, Pryce is a perfectly pleasant and decent man, and Lt. Surge, while cocky in the games, isn't nearly as mean about it as he is in the anime. All of them make friends with the heroes in the end. However, others, like Brock, Misty, Cilan, Iris, and Clemont, join Ash as protagonists and are more openly heroic characters.
Pokémon Special has a downplayed example with Norman. In the games, Norman is a kind, gentle person who respects his child's wishes and would most likely not use physical violence. In the manga, Norman is a lot meaner and beats up his son for disobeying him. Despite his harshness, he is on the side of good - he is genuinely supportive of Ruby.
Ocasionally used with the Pokémon themselves (particularly either Poison or Dark types), such as in the Mystery Dungeon games. In the games and anime, even Pokémon seen working for the antagonists generally aren't actually evil, just taking orders from their trainers, and aggressive wild Pokémon are only animals obeying their instincts. While genuinely evil Pokémon do exist in the anime (such as the Malamar in XY and an unusually mean Togepi in Diamond and Pearl), they are a minority and not representative of their species as a whole. However, even in Mystery Dungeon, you can recruit Pokémon like Ekans and Skuntank into your team and the species itself isn't portrayed as Always Chaotic Evil.
Giovanni was the head of a yakuza in the games but made a Heel–Face Turn after being beat by Red. Giovanni in the anime never disbanded Team Rocket and is far more violent than his game version is portrayed.
In Pokémon Black and White, N is a very sympathetic Anti-Villain with good intentions. He eventually makes a Heel–Face Turn in the sequel games, helping the player against Ghetsis, his much more evil adoptive father. However, in Pokémon Special, N has fewer redeeming qualities and manages to convince White's Tepig to leave her. His goal also seems to be more like Ghetsis' goal than in the games.
Team Galactic is hit by this in the anime. They're a good deal more sinister and self-interested than they were in the games. Cyrus in particular becomes a lot more malevolent, with his altruistic acts and qualities removed, and his tragic backstory never brought up.
In Pokémon Black 2 and White 2, Colress, while still a scientist in the employ of Team Plasma, does encourage the player and even gives them a device needed to progress further in the game. He is involved with Team Plasma For Science! and is not particularly interested in their goals, expressing distaste for Ghetsis. After his defeat, he encourages the player to stop Ghetsis' plans. In Pokémon Best Wishes 2 Episode N, Colress is a true Mad Scientist who experiments on Pokémon to the point of torture, uses mind control on the Pokémon in his introductory episode (including those of the main characters), and is more than willing to hurt Ash and his friends to prove his theories. He is also more appreciative of Ghetsis due to Plasma's "providing" increasingly more difficult "subjects" pushing the theories further. Colress in the game has a Heel–Face Turn, willingly disbands Team Plasma, and becomes The Atoner after Ghetsis is defeated, while his anime counterpart is arrested by Looker. The Anime counterpart does come up with the idea for a Pokemon translator, but after he's arrested and in a way emphasising his Blue and Orange Morality.
Team Plasma as a whole is subject to this in Episode N. While not a pleasant group in the games; Plasma is often engaged in moral debates about their intentions under Ghetsis, sometimes questioning their motives and splitting between leaving the group and becoming even darker after The Reveal of his true motives. In the anime; Plasma are outright villains with none of the moral conflicts they have in the games, fully supportive of Ghetsis' goals and posing avery large threat to Ash and his friends throughout their arc. Uniquely, this was deliberate by the writers as their initial appearance ended up being indefinitely postponed by the Tohoku earthquake and tsunami.
The Pokémon Special version of Colress is portrayed along the same lines as in the anime.
In Arceus and the Jewel of Life, while Marcus attempts to betray and kill Arceus using extremely heinous methods which have serious consequences in the future, he seems to genuinely believe that returning the Jewel of Life to Arceus will cause Michina Town to turn back into a wasteland and that his actions are necessary to prevent this. As it turns out, this is the case, but the inhabitants are able to restore the valley on their own. In the tie-in manga, his motivations are purely selfish - he wants to kill Arceus to become a god himself.
In Pokémon X and Y, Yveltal is a Dark Is Not Evil Pokémon who causes destruction as part of its life cycle, not out of malice, and seems to disapprove of its powers being used for unnecessary destruction. It teams up with the player to stop Team Flare's genocidal plans, just as its life-giving counterpart Xerneas does. In Pokémon: Diancie and the Cocoon of Destruction, it is the Big Bad of the movie who seems to take joy from deliberately sucking the life out of everything around it, and is more clearly a Dark Is Evil foil to the Light Is Good Xerneas.
Team Flare in the games are largely an Ineffectual Sympathetic Villain team in the vein of early Team Rocket with the exception of Big Bad Lysandre. In the XY arc of Pokémon Special, Flare ends up having their more malicious elements increased and their campier ones suppressed to the point of burning Vaniville Town to the ground in order to obtain X's Key Stone and Kanghaskhanite.
Team Flare in the XY and Z arc of the anime are portrayed similarly to their counterparts in Special.
Gendo Ikari: In the anime, he is Ambiguously Evil, he sincerely praises Shinji for his combat performance at one occasion, and with his Famous Last Words he regrets having been a bad father to him. In the manga adaptation, he is unquestionably evil, has a massiveGod-complex, and outright hates Shinji. In the manga, he's also implied to have personally killed Kaji, whereas it was unknown if he had anything to do with it in the anime, even though he was hinted at being involved somehow. He's somehow even worse in Neon Genesis Evangelion: Campus Apocalypse.
In the Mai-HiME manga, the main antagonists of the first arc are Haruka and Yukino, the latter of whom is friends with Mai and Mikoto in the anime, and the otherwise heroic Akira assists them. By contrast, Shizuru never turns Psycho Lesbian, and Nao (reluctantly) helps the heroes after the teams merge.
Kimblee, while an awful person in the manga, had his negative qualities cranked Up to Eleven, and his good ones suppressed.
Even Hohenheim, the Big Good in the manga, became a Retired Monster; instead of being tricked into helping Father turn the nation of Xerxes into a Philosopher's stone, and only becoming aware of the plan once it was too late to stop it, he and Dante turned people into Philosopher's Stones to prolong their lives.
Wrath and Envy were already horrible monsters in the manga, but the anime made them worse. Wrath (now named Pride) loses all of his Noble Demon qualities and his last scene involves him strangling his Morality Pet, his son, Envy had his sadism cranked to maximum, and both lose their Alas, Poor Villain moments.
Barry the Chopper, while Ax-Crazy in both the manga and original anime, was more of a neutral character in the former and even joins forces with Mustang before his death after realizing that he's going to be hunted down for his connection to the Fifth Lab anyway. The original anime's Barry unrepentantly sides up with anyone who can help him kill as many innocent people as possible, joining up on a mission to slaughter a settlement of Ishvalans forcing Scar to step in and put him down.
Yoki in both versions starts out as a small-time villain who ends up disgraced by the Elrics, which leads him to rat out Scar to reclaim his status. There the similarities end—the manga ultimately has him becoming a reluctant and (generally) not very helpful good guy, while the anime has him killed by Lust to incite a riot between the military and the Ishbalan refugees.
In a similar but lesser manner, Shadow the Hedgehog in the Sonic X anime. In the games, Shadow started off a vengeful weapon ready to destroy Earth's population in honor of his murdered friend. Throughout his story however, he is portrayed with a palpable sense of doubt and emotional conflict, before ultimately pulling a full Heel–Face Turn two games later. In the anime, he roughly follows his games counterpart's story, but maintains his more sinister neutral alliance and is The Unfettered to the highest scale (at least once perfectly willing to kill a child in cold blood, along with anyone who defended her, if it meant stopping a villain).
In the manga of Deadman Wonderland, the staff of the titular prison Hand Wave the prisoner deaths in the dog races by claiming that they are done with special effects. In the anime, the special effects angle is done away with; and the prison openly admits that many of the competitors do not survive and die brutal deaths.
Kaede Fuyou from SHUFFLE!. While not exactly a villainess, she did, in both versions, believe that Rin was responsible for her mother's death (a misconception he encouraged to prevent her from losing the will to live), and abused him for years until learning the truth, at which point she devoted herself to him in order to atone. In the anime, in which Rin canonically goes out with their mutual friend and senpai, Asa, resulting in him spending less time with Kaede (in part not wanting her to be consumed with him), she snaps and attacks Asa, causing her to collapse, but comes to regret this later. In the visual novel, after finding out that Rin and Asa are a couple, Asa apologizes, but Kaede sadly accepts their relationship, albeit with the scene being somewhat similar to Kaede and Asa's reconciliation from the anime.
In the original Yu-Gi-Oh! manga, Rex Raptor/Dinosaur Ryuzaki, while a bit of a jerk, doesn't cheat and he did have a more helpful and honorable side. The anime's version of Rex is closer to the manga version's characterization at first, but eventually associates with more villainous characters like Dartz and Weevil Underwood in a way that Manga Rex never did, and he eventually tries to steal Joey's soul.
Bonz/Ghost Kozuka in the manga is a Punch Clock Villain working with Bandit Keith, feeling that Keith trapping Yugi, Joey and the others in a cave to get them out of the Duelist Kingdom tournament was going overboard and getting an Alas, Poor Villain death when he ends up having the misfortune to duel Yami Bakura in the Battle City tournament. In the anime Bonz has no problems with Keith trapping the others in the cave and tries to cheat by stealing everyone else's duel cards during the Battle City arc, turning him into an Asshole Victim when Bakura runs across him.
In both the original and dub version, Daitokuji-sensei is an Anti-Villain using a façade to hide his true intentions, but the façade is much, much nastier in the dub. While in the original he spends his duel with Judai giving a Not So Different speech in which he compares Judai's Fusion Monsters with the ancient practice of alchemy, in the dub he goads Judai and tells Blatant Lies about his previous victories at the Academy being the result of rigged duels. (Which he admits was untrue after losing.)
Chosaku Manjoume, or Slade Princeton in the dub has a minor case of this. In the original japanese version, after he loses to Jun (Chazz in the dub), he tells Shoji/Jagger that their little brother has grown up more than they thought and grows respect for him. None of this occurs in the dub, and he's more annoyed that he lost if anything.
The Dark World Fiends were presented as villains in the third season, which contradicts the flavor text of some of their cards in the game and the Master Guide 2, which claims they are not evil. In fact, the flavor text on Zure, Knight of Dark World's card claims that he "never oppresses the commoners", while that's probably what he's most notorious for doing in the anime.
Also, in the manga version, Jim Cook is an antagonist who is far more malicious than his lighthearted and benign anime counterpart. It's not his fault, however; he's a Brainwashed and Crazy pawn of Tragoedia.
Like Daitokuji-sensei above, Yubel also got subjected to this in the dub. While she was still a terrifying villain in the original with many horrible deeds under her belt, she was ultimately motivated by her love for Juudaiand her desire for him toremember her. The dub turned her into a straight-up psychopath who wanted to "play" with him, and because it cut out Season 4, she never had her Heel–Face Turn.
In the manga version of Yu-Gi-Oh! 5D's, pretty much every character has a different background and personality, but Rua and Ruka more so than any other. They start of as villains in this version (and rather sadistic ones at that) very unlike the kind and innocent children they are in the anime. It is later revealed that Rua underwent a Duel Dragon ceremony to save Ruka from an illness, only Luna to become enslaved by the spirit of one of the Duel Dragons and for Rua to become Brainwashed by her. Eventually, Yusei is able to use his more benevolent Dragon to break the spell.
The Synchro dimension is modeled on the situation in Yu-Gi-Oh! 5D's, but the counterparts for Neo-Domino and Satellite, the Tops and the Commons respectively, are both worse than the originals. The Tops instigated the economic inequality themselves and are proportionally a much smaller group than their original versions (they make up 1% of the population, whereas the populations of Neo-Domino and Satellite were implied to be more even). The Commons buy into the Bread and Circuses act so thoroughly they not only support the worst aspects of their world, they insult and mock Yuya for speaking out against institutionalized slavery.
In the manga version of Chrono Crusade, Big Bad Aion is portrayed as misguided and possibly insane, but sympathetic, having turned to evil deeds in a desperate attempt to fix what he felt was a corrupted system after learning an Awful Truth. In the anime, he was turned into the literal Anti Christ.
Prétear: In the manga version, one of the Leafe Knights ( Sasame, the Knight of Sound) is strongly hinted to have been in love with the villain in the backstory, but he's definitively a good guy and remains that way for the entire story. In the anime, where Fenrir plays a bigger role, he eventually breaks down and becomes her minion because of his Mad Love.
Queen Beryl was a villain in the manga, but an ultimately tragic figure who was manipulated by Metaria into her crimes in her past and current incarnations, and ultimately doomed not by her villainy, but her own belief that she was beyond redemption at this point. In The '90sanime, she's a straight-up evil villain who willingly and loyally serves Metalia.
Although this is more of a case of Adaptational Anti-Heroism, Rei Hino/Sailor Mars is hit with this in the 90s anime. Rei seems more abusive towards her friends (especially to Usagi) in the anime than in the manga, especially in the first season. It's even worse in the DiC dub where Rei (or Raye as she is called in that dub) makes no qualms about wanting to kick Serena out of the Sailor Scouts and take over as the leader.
The first anime of Black Butler does this with Queen Victoria, of all people. In the manga she's a straight Cool Old Lady though she seems to like the idea of a Zombie army, while in the anime she's responsible for Ciel's parents' deaths, and planning to start a world war to "cleanse" the world with her angelic accomplice, Ash. It is, at least, implied that she's not at all stable, in part due to Ash's machnations.
Really, all of the Zeon figures except Ramba Ral are shown to be much more vile and cruel in Origin. Ramba's biological father and Char's mentor, Jimba Ral, was vaguely described as a loving father figure in the original anime. In Origin, Jimba is a borderline Conspiracy Theorist and Abusive Parent who may have shaped Char into a sociopathic Tyke Bomb. Likewise, Kycillia Zabi was originally portrayed as a stoic Chessmaster who acts out of loyalty to her family. Here, she is shown to be a violence-lovingManipulative Bitch who happily backstabs her own family members without a care in the world. Even Garma and Dolze were given more Kick the Dog moments though they are still considered the nicer Zabis.
The Cheshire Cat in the manga adaptation of the Kingdom Hearts series is outright villainous, compared to his more neutral role in his origin book and in the game. Maleficent even offered him a place in her group, but he declined.
Magi – Labyrinth of Magic: While Fatima is a ruthless slave trader in both the anime and the manga, both of which show him choosing to feed an Ill Girl potential slave to a pack of hyenas rather than simply give her medical treatment because it's "not worth the money," the manga also shows that he himself was once a slave who was broken down and made loyal to his mistress Umm Madaura, who, among other things, sold him as a Sex Slave to a male client. The anime completely edits out his rather horrific backstory, making him an utterly unsympathetic Jerkass.
An odd example comes with Anchovy, since the manga was released before the anime showed her match with Oarai. In the anime, Anchovy's competitive but fairly good-spirited, and after losing, invites the Oarai crew to eat with her and the people who set up the match. In the manga, she starts off by accusing Miho of having a "weak" way of tankery, and at the end, accuses Miho of costing her old school the championship by abandoning the flag tank.
Erika is a Jerkass in the anime, but mainly to the extent of being snide and condescending toward Miho (for example, in the finals, saying that Oarai must be weak if she became its commander). In the manga, between the semifinals and the finals, Erika flies over to Oarai, confronts Miho, and angrily accuses her of not just costing them the victory, but abandoning them in their time of crisis, and vaguely insinuates that Miho traded her vice-captaincy of her old school for captaincy of her new school. She's significantly more vicious and angry in that scene from the manga, and leaves Miho in tears at the end of it.
In the Bokurano manga, Koyemshi/Dung Beetle is quite a jerk throughout, but he has a few Pet the Dog moments, such as performing a Mercy Kill on his sister, Youko, and giving Ushiro reasons to fight. In the anime, he's significantly more vicious, including mocking one of the dead kids, was quite a Dirty Cowardwhile he was a human and ultimately gets killed by his aforementioned sister when he tries to force the youngest of the group into the game.
InuYasha: Izumo/Gyu-oh of episodes 94 and 95. The English dub of those episodes makes him a full-fledged villain, whereas the original Japanese made it clear that he was a Tragic Monster who was just driven by his madness.
Annie Leonhart from Attack on Titan is a ruthless killer in both anime and manga, but the manga goes further to portray her Anti-Villain status, giving her more humanizing moments such as genuinely smiling at one point, mentoring Eren Jeager in hand-to-hand combat, and also looking visibly shaken when she accidentally kills civilians. All of these moments are removed from the anime while also increasing the number of people she kills. It's not unusual to hear people say they hate her after watching the anime, then they read the manga and start sympathizing with her.
More like "Adaptational Antagonism", but Leon Mac Nicol in the Bubblegum Crisis OVA was supportive of the Knight Sabers, but much like George Stacy towards Spider-Man in relationship to their comic counterparts in The Amazing Spider-Man, Leon in the Tokyo 2040 remake considers the team vigilantes and a blight on the AD Police.
While Light Yagami was always a Villain Protagonist in the anime and manga, he started out sympathetic and well-intentioned. In the live-action films, he ends up Jumping Off the Slippery Slope much sooner than in the anime and manga, to the extent that unlike his anime/manga counterpart, he's perfectly willing to personally kill his own father to prevent the Death Note from being analyzed.
While Ryuk could hardly be considered a hero in the anime or manga, he's much more monstrous in the live-action TV drama. In the anime/manga, he just randomly dropped the Death Note and Light picked it up by chance, with Ryuk just kicking back and watching as Light carried out his plans. In the TV drama, he deliberately drops the notebook near Light and serves as The Corrupter, goading Light into killing more people when he hesitates, effectively making him responsible for Kira's existence.
L is likewise subject to this in the TV drama. Though not exactly a 'hero' (with Word of God admitting that he's a bit evil), he usually comes across as A Lighter Shade of Gray when compared to Light and a few spin-offs (namely the film L: Change the World and the light novel Another Note) portray him more sympathetically. The drama by contrast draws more attention to the amorality of his actions and he generally is far more smug and arrogant than most portrayals.
In his debut in Battle of Gods, Beerus was goofy and likable, though he did have moments of being a Jerkass God. Here, his more sympathetic qualities are toned down while his Jerkass God aspects are ramped up, doing such things as actively destroying planets after eating all their food, outright saying he never gets tired of watching planets explode after he blows them up, and going out of his way to be a dick to Vegeta and intimidate him after crashing Bulma's birthday party. Most notably, unlike in Battle of Gods where his slapping Bulma was more reflexive than anything, in Super, after Bulma slaps him, he actually turns towards her and outright backhands her across the face, all with a Slasher Smile and a glint in his eye. After the Battle of Gods adaptation, Beerus is made more in line with his film counterpart.
This occurs in-series in Yo-Kai Watch. When Komasan reveals to a mangaka that he is really a yokai she uses him as inspiration for her manga. Sadly it is a horror manga where he is a big, scary monster instead of the cute Cartoon Creature he really is.