Quite a few fans think Victor Van Dort from Corpse Bride ended up with the wrong woman and Emily was more compatible with him; at any rate, he'd gotten to know her far more than Victoria.
The Secret Of NIMH has Justin and Mrs. Brisby. Some fans tend to mistake Justin's chivalry as romantic advances on the widowed female of another species. A rumored storyboard depicting the two of them kissing only escalated matters (but Don Bluth debunked it as a hoax).
In Tinkerbell, Terrence was supposed to be Tink's love interest, but a significant portion of the fandom thought he was a pretty boy caricature, and thought that Tink/Bobble was much more appealing.
Kung Fu Panda fans seized on the obvious hints throughout the franchise (especially in Kung Fu Panda 2) and have embraced the Po/Tigress coupling, eager to see it progress.
Historically, Rolfe does marry Pocahontas, but fans of the Disney version think she belongs with John Smith (a sentiment that even The Walt Disney Company clearly shares anyway).
Felidae has Francis/Felicity. Which might have happened in canon had Felicity not been gruesomely beheaded.
Some fans of Paprika have lots of trouble accepting that Chiba loves Tokita, and would rather have had her end up with Konakawa. This ignores how the fake ending with Konakawa and Chiba kissing in the sunset is supposed to be making fun of trite, cliché movie endings, which implies that pairing them together would have made for a really, really bland and predictable ship.
Para Norman has very questionable one - Norman and Aggie. Some find the Shipping weird because they are related, but it is also justified because of three hundred years of genetic separation. Also, the song Little Ghost in the credits really enforces it.