Since Victor from Corpse Bride spent a lot more time with the Corpse Bride herself, rather than his actual love interest, that pairing is a lot more popular.
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.
Historically, Rolfe does marry Pocahontas, but since the original film is considered vastly superior in quality and is obviously much more popular than the direct-to-video sequel, John Smith and Pocahontas endure as a more popular pairing. Evidently Disney agrees, as much secondary and merchandising materials make no mention of Rolfe.
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.
ParaNorman 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.
The Yaoi Fangirl faction of Road To El Dorado is, unsurprisingly, siding with the Tulio/Miguel pairing, due to the closeness and chemistry of the two main characters. Fueling this are various stories that they were intended to be a gay couple, before being vetoed by hire-ups.