The Aracuan Bird from The Three Caballeros is pink, unlike its real world counterpart the Plain Chacalaca, which is more of a dull brown.
A few of the reviews for An American Tail when it first came out complained about how un-catlike Tiger looked.
Shifu◊ the red panda from Kung Fu Panda, with his huge round ears, more whitish orangey fur, and dark brown hands, is not that easy to identify as a red◊ panda◊, which has medium sized, rounded triangular ears and is more reddish with a black underside and legs.
Zilla, a.k.a., the American Godzilla, is an interesting variation. He's supposed to be a mutated marine iguana, but his physical structure is more akin to that of a theropod dinosaur. Of course, since he is mutated, this might be justified.
Ironically Godzilla himself , who was in fact supposed to be a mutated theropod of some variety, doesn't really look like any real dinosaur so much. Part of this is Science Marches On, since back in the 50s when Godzilla was created, the classic 'tripod' pose for theropods was still in vogue, but even taking that into account, his head is way too small to be a theropod.
Anguirus in Godzilla Raids Again, despite the claims of the contrary, doesn't really look much like an Ankylosaur.
Averted in early artwork where Pumbaa is certainly a warthog.
Jiminy Cricket from Pinocchio is so heavily anthropomorphized that he looks more like a little green man with a rabbit nose and no ears. Animator Ward Kimball, who designed him, admitted that "he's a cricket because we say he's a cricket." And then the live-action adaptation actually had him as a tiny human.
Remember the fact that Ratigan actually hates being called a rat? Wordof God confirms that he is indeed a mouse, but for some reason he looks like a rat. Hint? Just count the number of fingers!
Flounder in The Little Mermaid is portrayed as a large yellow fish with blue fins and stripes and nothing like actual flounders (which are large, flat brown fish whose eyes are both on one side of its face) at all. However, that could just be his name, not his species. Also, many of the species described in the song "Under the Sea" look nothing like their real-life counterparts.
And the aardvarks look more like giant anteaters with mouths at the base of their snouts and big ears.
The Triceratops from the third film look more like Chasmosaurus or Torosaurus due to their large frills. Also, the Kentrosaurus look more like Miragaia and the Troodon look more like Compsognathus.
Roger, Buck's pterosaur mount, is apparently a Harpactognathus. However, her crest is more similar to a Pteranodon's.
Despite being claimed by the creators to be a Baryonyx, Rudy, the Big Bad of the third film, doesn't look all that much like this genus. He exceeds Spinosaurus in size (in Real Life Baryonyx was only about 7 or 8 meters long), and has several exaggeratedly crocodilian features such as bony scutes down his back and nostrils at the end of his snout.
Silas the petrel from the fourth film has feet like a blue-footed booby.
Sid the Sloth is supposedly a Megalonyx. While identifiable as some form of sloth, Sid looks fairly different from any known species.
Kron and Bruton from Dinosaur are supposed to be Iguanodons like Aladar and Neera, but Kron looks more like an Altirhinus and Bruton looks more like a Muttaburrasaurus since real Iguanodons do not have nose crests like they do.
Aladar and Neera, for that matter, possess flexible lips instead of beaks. This detail apparently was changed after it was decided that the characters would speak (in the original draft, the only spoken lines came from a narrator) and it would have been too difficult to get the Iguanodon beaks to look good while moving in such a way.
Frankie the flea from Tom and Jerry: The Movie for some reason actually looks more like a large green mosquito than an actual flea. Also, fleas aren't the same size as mice!
Similarly, the largest member of the Singing Cat Gang actually does not look like a cat at all and looks more like a gorilla instead.
Priscilla from Rango is supposed to be an aye-aye, but she actually looks more a mouse instead. This has led to conflicting info on her species — logically, she can and should be a cactus mouse, but Word of God on the DVD commentary says aye-aye.
Rango's love interest Beans is supposed to be some sort of reptile, but she looks more like an...alien...thing...
Chirin's adult form at the end of Chirin No Suzu is supposed to be a ferocious ram, but he vaguely resembles more of an ibex or a goat instead and nothing like the other sheep in the film, not even himself as a lamb. As a result of this, at the end of the film, he ends up being chased out of his own farm!
Narrator: ...but to them, he was neither ram nor wolf, but a monster...
The large theropod featured in the "Rite of Spring" segment of Fantasia is supposed to be a Tyrannosaurus rex, but it looks more like an Allosaurus instead.
In a similar case, the epononymous Allosaurus from The Valley of Gwangi looks more like a T. Rex with three fingers.
As noted by many youtube commentators of Felidae, Kong is decidedly dissimilar to the more anatomically correct cats that populate the movie, looking more like a bufallo/bull-dog hybrid than an actual cat.
Baloo from The Jungle Book is supposed to be a sloth bear, but he doesn't even look like one at all! The only indication that he's a sloth bear are of course, the long, sharp claws unique to that animal.
The Chilantaisaurus from You Are Umasou barely looks like the real animal in that it has bull shaped horns and a short, rounded snout (which led to some viewers mistaking it for a Carnotaurus). At least it's the same size as Tyrannosaurus and retains the huge arms and claws.
Most of the dinosaurs in the movie don't really look like their real-life counterparts, especially the Tyrannosaurus and Maiasaura. The Triceratops, Protoceratops, and Parasaurolophus are exceptions, however.
The bit with the Chilantaisaurus may be Hand Waved, in that no decent skull material of the dinosaur has been found yet.
And to be fair, the tyrannosaurs have a similar looking snout as well.
The Sarco Brothers from Dino Time are supposed to be Sarcosuchus as their name suggests, but they look more like mutated crocodiles instead.
The titular character of Bolt is supposed to be a white German Shepherd and from the looks of it an adult. One of the most noticeable errors is he's way too small. He's barely larger than a cat. There's concept art◊ of him looking much more accurate than in the final product.
The titular mischievous alien from Lilo and Stitch looks absolutely nothing like a dog. Even In-Universe none of the townsfolk are particularly convinced despite Lilo's insistence of him being a Collie dog who got ran over. At one point in the film Lilo's sister, Nani, flips through a book of dog breeds and notes that Stitch might be an evil koala. One of the comics from the Disney Adventure Archive, where Lilo takes the disguised Stitch to a vet for his checkup, had the veterinarian take one look at Stitch and point out to Lilo that he didn't look anything like a collie or anything else he'd ever seen before (even showing her a picture of the breed).