"As many people have noted throughout the years though, Disney has been rather...lax when it comes to adapting books and fairy tales into movies. This is understandable in some cases. Still, it can be a bit galling when one knows that the fire-breathing, demonic witch on the screen was a kindly old lady in the source material."
Fandom has a specific term for taking a character that is good (or neutral) and downgrading them to villain: Ron the Death Eater
Sonic The Comic Online does this with many games characters. Shadow, Rouge, the Babylon Rogues, Bean, Silver... even Cream the Rabbit! Blaze is immune to this, being almost identical to her game counterpart.
While Discord in canon was certainly malicious and powerful, he was presented more along the lines of a misbehaved brat than anything else and he did ultimately have a Heel-Face Turn, starting in Season 3 with a friendship with Fluttershy and occasional helpful, if still jerkish, Trickster Mentor moments. It was completed in the Season 4 finale after a backslide prompted by Tirek and a Heel Realization after Tirek backstabbed him. The episode shows that Discord is capable of remorse when he genuinely and seriously apologizes for his bad behavior and completely reforms. However, many fan stories (most prominently the Pony POV Series and The Nuptialverse) present him as an unrepentant Ultimate Evil, responsible for multiple genocides and creating the Changelings, among other crimes. (This is somewhat more justified for fanfics that were written before "Keep Calm And Flutter On" and the character development Discord got in that episode; more modern works have less of an excuse.)
While it's mostly tongue-in-cheek, Princess Celestia gets this a lot. There are memes of her being a tyrant who rules with an iron hoof and sends people to the moon at the slightest annoyance, a Discord-like prankster causing the cast's problems for the fun of it, or a Memetic Molester. Look up Tyrant Celestia, Trollestia, and Molestia, respectively.
Damion, a one-shot character from Pokémon, was originally just a Jerkass becomes a dangerous psychopath in Symbiosis. He is willing to kill Ash to get revenge on Brock and Misty for reporting his crime.
In the Simpsons AU The Fourth Simpson Child, Lisa gets this treatment, going from a socially isolated smart girl who is somewhat The Unfavourite to a Smug Snake who is openly jealous of Samantha (her older sister and the titular character).
In Touhou, Wriggle is just a run-of-the-mill insect youkai and, while still dangerous, she usually has no malicious intentions against humans and will attack only if provoked. In the fanfic No Such Thing as Fairy Tales, Wriggle is a fae, who spirits aways humans and torture and rape them for no other reason because she can. An Eldritch Abomination.
Touhou Ibunshu does this to almost half of the cast. Rumia, Mystia, and Remilia are Creepy Children that eat people, Cirno, Wriggle and Hina are sadists that try to kill people for no reason, Sakuya is a Serial Killer and succeeds in killing the humans, and Yukari and Mokou both try to obliterate Gensokyo. Strangely, the ones that get some Character Development end up being more sympathetic than the originals, even if they are worse people overall.
Imperfect Metamorphosis takes Yuuka Kazami (a powerful and dangerous individual who nonetheless mostly leaves people alone) and turns her into The Dreaded who makes every character crap their pants whenever she's mentioned, and more than lives up to her reputation by being a full-blown Outer God.
In Rainbooms and Royalty, which is the re-imaging of the pilot, Nightmare Moon is more explicit in her attempts to stop the Mane 6. She assaults and repeatedly tries to kill them especially Rainbow Dash, brainwashes Shining Armor and Ditzy Doo into her loyal minions, offers Rainbow Dash a greater temptation than she received in canon, and in a final act, threatened to drop the rest of the Mane 6 to their deaths and forcing Rainbow Dash to choose which ones to save. By the end, it is not surprising that Rainbow Dash hasn't forgiven Luna.
In Hot Heads, Cold Hearts, and Nerves Of Steel, King Sombra, who was already a Crazy-Prepared and evil dictator in canon, is more of a threat, since his actions have direct impact on the protagonists. He kidnaps the foals of Ponyville and brings them to the Frozen North. When Rainbow Dash reaches his lair he enters Rainbow's head and tells him his backstory: he started out as just as snobbish prince before he obtained the Alicorn Amulet. Afterwards, he sought even greater power, he murdered his wife, manipulated Luna into falling in love with him, and even after his defeat by the Princesses, he knew he had driven Luna into the despair that would create Nightmare Moon. He then reveals his plan, to sacrifice the foals to increase his power and become an alicorn god. And he comes pretty damn close as well.
In Freedom Through Harmony, Celestia is corrupt and banished Luna for trying to reason with her, that still does stop her from becoming Nightmare Moon though.
In I'm Here to Help, the senshi of the future, as well as Neo-Queen Serenity, are portrayed as considerably more villainous than their canon counterparts. While we don't see much of them, it's established that they are essentially the Big Good of the future, to the point where they were willingly asked to rule the now-united Earth. In the fanfiction though, their adoration comes from Neo-Queen Serenity "purifying" all negative emotions out of them, allegedly turning them into placid zombies. While Emerald is something of an Unreliable Narrator due to being insane, one segment told from the point of view of the future Jupiter and Mars has them discuss how they attacked/killed several children who Emerald had help with one of his plans, dismissing the whole thing as the children having made their own choices in the matter. Needless to say, the canon senshi would never willingly harm children, whether or not they were helping a villain.
The first and second victims, while acting similarly to how they did in canon (Hoping to kick-start the mutual killing and planning a murder so that Kuzuryuu can gradaute, respectively), they come off as somewhat less sympathetic, since their motives are revealed after their deaths.
The second murderer, and the first who's different than canon, is Sonia Nevermind, who not only never killed anyone in canon, but was also one of the nicer cast members.
In Kitsune no Ken: Fist of the Fox, Utakata, Yagura and Gaara are the three most villainous members of the Kyuushingai introduced, with Utakata being an Ax-CrazySerial Killer who'll even murder children in his rampages, Yagura being a cold-blooded gang leader who's infamous for making witnesses set to testify against him "disappear," and Gaara being an aspiring drug kingpin who's currently in an alliance with Yagura. Contrast their canon counterparts from Naruto, where Utakata was merely disillusioned after being mistreated due to his jinchuriki status but wasn't otherwise stated to be evil, Yagura only had his bad reputation because he was manipulated into committing bloody actions during his time as the Mizukage, and Gaara is one of Naruto's staunchest friends and allies (though he did start out Ax-Crazy and only wound up undergoing a Heel-Face Turn following being defeated in combat by Naruto).
The same fic also has Konan, who's a member of Akatsuki and determined to kill the Kyuushingai no matter what (in canon, she's also a member of Akatsuki, but there she's a Well-Intentioned Extremist who later becomes one of Naruto's supporters).
In the original story of Saint George and the Dragon and most reworkings of it, Saint George is the hero. For example, in The Reluctant Dragon, he becomes the title character's friend. Even in retellings where the dragon is Spared by the Adaptation, George usually convinces it to Heel-Face Turn. In the Dragon Keepers series by Kate Kilmo, Saint George is a Villain with Good Publicity who enslaves magical creatures and drinks dragons' blood while the princess he saved is an evil witch. The dragon from the original tale tells his own side of the story, in which he was a benevolent sorcerer betrayed and killed by George.
Myth-O-Mania has some in-universe examples: When Zeus rewrote the stories of Classical Mythology, he exaggerated monsters' scariness to glorify the heroes. (eg, The Minotaur went from being a vegetarian to eating humans.) Plus, Zeus claimed that Hades kidnapped Persephone, when actually she hitched a ride on his chariot while running away from her overprotective mother.
The mice from The Hitchhiker's Guide to the Galaxy - In the radio play, they are fairly amiable, and upon discovering that Arthur is in the ideal position to find the ultimate question, offer to make him "a reasonably rich man" if he does. In the book and subsequent adaptations, however, they are much more sinister, plotting to steal his brain in order to read the question from it.
Likewise, the Wizard is not necessarily a good guy, and does several reprehensible things, but when Greg Maguire got his hands on Oz, the Wizard became a power-seeking, first-rate Magnificent Bastard who exploits religious factionalism and Fantastic Racism to pit his potential enemies against one another, drive Oz into civil war, and start genocide of the sentient beasts as a cover for him trying to locate the Grimmerie and obtain absolute power.
In Alice's Adventures in Wonderland, the Queen of Hearts is clearly a mean woman and a blustering Jerkass type, but calling her evil might be stretching the definition a little; though she often calls for people to be beheaded, her husband secretly pardons most of the people she condemns, and the Griffon tells Alice that, "It's all in [the Queen's] fancy, you know. They don't actually execute anyone." Nonetheless, you can be sure in almost any modern story where Lewis Carroll's heroine is portrayed as the protagonist, the Queen of Hearts (often conflated with the Red Queen) will be the villain, and portrayed as far more evil than Carroll could have ever imagined. Whereas Alice's trial in the book ends with her realizing that the Queen of Hearts' threat against her is empty and dismissing the Queen's court as a pack of playing cards, in the 1951 Disney version, the Queen of Hearts is portrayed as a genuine threat, and the trial ends with Alice running for her life from the Queen and her soldiers before waking up.
The Jabberwock is often both this and an Ascended Extra in such works, seeing as the beast barely even counted as a character in Through the Looking-Glass, only briefly appearing in the now-famous poem that Alice read. The poem became so popular that most modern works include the creature as an adversary for Alice and the heroes in general.
In the picture book The Butterfly Ball, Sir Maximus Mouse, the cheese tycoon, is simply a workaholic who's too busy to go to the Ball. In Roger Glover's concept album adaptation, he's a borderline-demonic Corrupt Corporate Executive.
Aside from a fight when she premiered in one issue of the Comic Book, the Black Widow has never been a Spider-Man villain. Yet Gottlieb's The Amazing Spider-Man pinball has her on the backglass along with Spidey's other rogues, such as the Vulture and the Green Goblin.
In Zen Studios' Spider-Man pinball, J. Jonah Jameson is elevated from an annoying nuisance to one of four villains for Spider-Man to fight.
The Wizard in The Wonderful Wizard of Oz, although he becomes one of Dorothy's friends, isn't nice in his early appearances (after all, he did have Ozma kidnapped to prevent her from interfering with his takeover of Oz). However, in the Perspective FlipWicked and its musical adaptation, he is much worse. The musical version, though, is more sympathetic than the book version, who doesn't shy from personally murdering the Ozma Regent, violently suppressing Animal protesters, and attempting to exterminate the Quadlings just to get at the rubies on their land. In the musical, he's a sort of a Well-Intentioned Extremist who is puppeteered by Madame Morrible and generally seems to want the best for Oz, as long as he remains its leader.
This happens to several characters in Love Never Dies, the sequel to The Phantom of the Opera. The trope applies in two ways, both because characters from the first musical undergo villain transformations and because in The Phantom of Manhattan (the Frederick Forsyth novel that was the result of early work on what became this show) contains no such transformation, instead having the villain be a completely new character who didn't make it to the stage.
In Wonderland: Alice's New Musical Adventure, the Mad Hatter becomes female and the play's main antagonist, with the March Hare as her Dragon. In the book, he's scatterbrained, but not particularly malicious about it.
In The Golden Ticket, an opera adaptation of Charlie and the Chocolate Factory, Spoiled Brat Veruca Salt agrees to a deal with a TV reporter to secretly film and photograph the titular, top-secret factory during the Golden Ticket tour — which makes her and her dad, who goes along with the plan, spies. As well, she's much nastier in her selfishness than in other versions, and specifically contrasted with poor-but-good Charlie Bucket throughout. With this in mind, while the novel and all other adaptations have them the third group to be eliminated from the tour, here they're the fourth and last to go.
In The Ring of the Nibelung Hagen goes through this. He is largely a Composite Character of Hagen from The Saga From The Volsungs and Literature/Nibelungenlied. However in the Volsung Saga he is Gunther's heroic brother and though a more villainous figure in the Nibelungenlied, murdering Siegfried, there he is acting out of loyalty to Gunther. In the Ring Cycle Hagen is the son of the main villain Alberich and murders Siegfried and Gunther for the Ring of Power.
When it comes to other characters, the extras actually contain a spectacular Inversion. One strip features a man who stuffs minus in a briefcase after luring her in with promise of sidewalk chalk, and who would certainly have tried to abduct her if he wasn't stopped. His counterpart in the extras, on the other hand, is an innocent bystander who doesn't do anything to deserve being antagonized by the villainized minus.
This page lists five well-known characters who were reimagined into villains through Disney movies in this way.
The Day of the Barney Trilogy takes Barney and Baby Bop, who are portrayed as sincere and good friends to the kids on Barney & Friends, and portrays them as villains who successfully get the world's children to kill any adult they come across, kill their male Special Friends when they turn thirteen, and take the thirteen year old girls away to fatally mother mutated offspring. They're even revealed to be Really 65 Million Years Old and to have been the harbringers of many of the world's evil dictators and catastrophes.
Hilariously, the Lighter and Softer version of the game Warhammer 40,000, Brighthammer 40000, does this to the Tau Empire. To explain, Warhammer 40000 is an extremelygrimdark setting, with a number of genocidal, xenocidal and one or two omnicidal factions locked in a Forever War. The sole exception is the Tau, who are still bad in a sense but still the most sane and sympathetic of all factions. For Brighthammer 40000, every faction except the Tau have been made more sympathetic, while the sinister aspects of the Tau have been played Up to Eleven, along with some new ones added. This has the effect of turning the Tau into the setting's Big Bad. Water Caste Tau are all conniving schemers and cheating merchants, Air Caste Tau are all cowards who launch unprovoked bombing runs and orbital strikes on defenceless worlds, Fire Caste Tau are all violent brutes who bully other Tau and use prisoners of war for target practice (when they bother to take prisoners at all), and the Ethereals run the empire as this horrible 1984-esque society and often use mind-control to order Tau to kill themselves, sometimes for fun. Only the Earth Caste escape this treatment, being poor schmucks who are abused, exploited and left to die when they're no longer useful.
The Midwestern Brotherhood of Steel are just downright fascist in one of the worlds from We Are Our Avatars, they even tortured an Enclave soldier even though he's a Punch Clock Villain.
Danganronpa Abridged Thing does this to the first murderer. In canon, the crime was committed in what was arguably self-defense, although it's pointed out that the killer technically went out of his way to get to and finish off the victim. In the abridged series, the murderer accepted the victim's invitation, hoping to "get some," and killed her when she called him a "weenie."