Will Turner from Pirates of the Caribbean. Ever since he married Elizabeth Swann, many viewers who wanted Elizabeth to be with Jack Sparrow are making him out to be a rapist, an abuser, too "nice" so the Super Bad Boy is OMG better, or both.
Calypso gets this from Davy Jones fangirls, who make her a horrible bitch. Granted as a pagan goddess and physical manifestation of the ocean she was hardly the most sympathetic character in the movie, but that's ignoring the fact that Jones himself wasn't very nice in turn (having her magically bound to human form, which she describes as "torture") as well as the fact that she clearly did still love him and was horrified to hear what he did to her. One Mary SueSelf Insert fic has said Sue actually kill Calypso, and be treated as a heroine for it. Which goes against everything in the trilogy's universe, but logic be damned.
This trope is inverted for Corpse Bride: Victor/Emily shippers want Victor to die — because Emily is dead from first meeting. That said, there has been a fair amount of vilifying of Victoria in post-film Victor/Emily fanfics, portraying her as a gold digger or just plain mean to Victor. (And it can probably be argued that leaving Victoria at Barkis's tender mercies in some AUs is A Fate Worse Than Death.)
Ever since The Lord of the Rings books were made into movies, Arwen has been loathed by Éowyn teenyboppers who see her as the obstacle for Éowyn to get Aragorn's love, or as a "bad, bad, girly girl". The Aragorn/Legolas slashers also have it against her. The animosity towards Arwen since the movies continually frustrates many book!Arwen fans.
Faramir also gets some flack from rabid Aragorn/Éowyn fans, who see him as being less worthy of her than Aragorn. Never mind that Aragorn himself sank that ship by pointing out how unhappy Éowyn would've been if she married him, and later was very happy when she and Faramir became the Beta Couple...
And both Éowyn and Arwen catch heat from the Mary Sue creators who ship their unholy spawn with Aragorn or Faramir. They get even more from the Yaoi Fangirl contingent who must have Aragorn sidling up to Legolas. (Or Boromir, which is a doomed relationship if you don't go severely AU.) In one fic, Arwen was turned into such a shrill harpy that, in a post-series tale set in the present day, she sold the mummies of her and Aragorn's children to a museum just to hurt him. (Seriously)Éowyn is likely to get written off as "that butch chick".
That was Bagenders, and mostly done for Rule of Funny and parody, as literally everyone is taken to the extremes of their character, or just blatantly out of character. Faramir is mostly painted as a bit weak (Boromir on one of his visits from the afterlife ignores a note from Faramir asking him to come back and help him on the grounds that 'she's probably pulling his hair again').
Adding to the weirdness factor of the whole Aragorn-versus-Faramir argument is the reason that Tolkien didn't stick with his original Aragorn/Éowyn. Faramir is an Author Avatar, and reportedly, Tolkien grew to love the character of Éowyn so much that he changed his plans just so she would end up with his Middle-Earth doppleganger.
The Sweeney Todd Sues, who somehow manage to become Sweeney's truest of true loves ever, even though (A) he was utterly devoted to Lucy throughout the movie and (B) Sweeney was very much anti-touch. One such Sue actually got Sweeney to denounce his love for Lucy and Mrs. Lovett after both were dead, in favor of said Sue.
Due to Bollywood marketing being dependent on which combo of actors and actresses is the screen couple (referred as a "jodi" by Indians and the Industry), fans of a particular screen couple (who often do several movies together if successful) will fight fans of another couple. Shah Rukh Khan/Kajol is the quintessential example these days.
A good number of fans ship Hiccup with Toothless (yes, the dragon) or Tuffnut (Ruffnut's twin brother) with as vehement loathing of Astrid, who tends to get labeled as shallow for showing interest in Hiccup after finding out about his dragon, even though she was the only teen that did not actively mock/tease Hiccup in the beginning and thus had less of a personality shift than the others would have.
Many fans of A Knight's Tale would have preferred that William ended up with Kate rather than Jocelyn. Also uses "feminist" bases since the fans like to take the Plucky GirlWrench Wench and then "give" her William as a "prize" for being a "strong female and so unlike that Jocelyn bitch"... when if they believed in Kate's strength as a character as much as they said, they wouldn't feel the need of making Kate's overall happiness depend oh so much on whether the hero liked her or not rather than on other things like her own blacksmith work.
Poor poor, poor Carly Spencer. It's bad enough that fanboys want the actress who plays Carly (Rosie)'s head chopped off for replacing Megan Fox (something that Rosie obviously has no control over, she took the role, as any sane person would do if they were offered a role of a lifetime in a big budget movie like the 3rd Transformers movie), but according to hardcore SamxMikaela shippers, she is ugly (Yes the Victoria's Secret Model is ugly...don't think too hard about that), evil and the anti-christ who should be burned. It doesn't help that Mikaela is only mentioned in passing in the 3rd film, and it's implied that she dumped Sam because she only liked him for his involvement with the Transformers...
This somehow managed to happen with non-canon pairings in The Avengers fandom — many Steve/Tony fics depict Bruce as an emotionally abusive coward who's only with Tony because Tony protects him; while many Bruce/Tony fics depict Steve as a self-righteous, bigoted asshole who treats Tony like shit or slut-shames him. And then there's the Loki/Tony ones where Pepper/Steve/Bruce/whoever is bashed so that Tony can run into Loki's arms, or Thor (who is depicted as being in a relationship with Loki, although the two are brothers) being bashed so that Loki can run into the arms of Tony. And before you ask, no, there are no shipwars that do not include Tony.
Usually averted with Pepper - she's a popular enough character that fanfic writers will usually just pair her up with whatever guy Tony isn't banging, most commonly Bruce. Usually with hilariously little build-up considering they never even spoke in the movie.
Speaking of the MCU, lots of fangirls tend to do this with Theoric, who in the comics was engaged to Loki's wife Sigyn before Loki pulled a Uriah Gambit on him. If Theoric shows up in an MCU fanfic, he's almost always an abusive asshole who deserves to get Uriahed, despite the original comic story actually had some of Sigyn's friends complaining he was too noble. This is especially hilarious because the fangirls could always just, you know, not bring him into an MCU story since he's a comics-only character with no basis in mythology.
Similar to the above, Mockingbird gets this from BlackHawk shippers, despite not even being hinted at in the films, and being a fairly popular character in the comics. When she's brought in to a BlackHawk fic, she'll either be a cheating, lying, obnoxious Alpha Bitch-type, or Clint's ex who broke his heart and is thoroughly bashed and tortured by Natasha for this.
Sky High fandom is small and pretty much dead, but it had a bit of this in its heyday, usually going after either Gwen or Will. Gwen was typically bashed for being "too girly" to justify Will/Layla (interestingly, the fact that she ended up betraying everyone rarely gets brought up here, nor does Lash doing the same thing stop him from having an armada of fangirls), when Will himself isn't torn into for being "bland" or falling victim to speculation that he'd be a neglectful boyfriend to Layla, in favor of Warren/Layla.
Disney sequels are already mostly despised for prettylegitimatereasons, but there's one sequel that really takes it too far, according to most fans. Pocahontas II has the audacity to break up the Official Couple of Pocahontas x John Smith and make the protagonist fall in love with John Rolfe instead! It's only logical Disney fans have this kind of reaction, and most refuse to acknowledge the existence of the sequel in the first place.note Of course, the Real Life Pocahontas did in fact marry John Rolfe, but come on.