In a short scene in Shrek the Third, Puss in Boots tries to flirt with normal, meowing female cats.
In Howard the Duck, the eponymous character flips out when he is served a breakfast that includes fried eggs. Howard's behavior is justified because he was accidentally abducted from a world populated with anthropomorphic ducks like himself, so the eggs "always remind him of his birthday", despite being chicken eggs.
Subverted in Surf's Up. The resident chicken is offended whenever someone comments that a delicacy "tastes like chicken".
In Rock-A-Doodle (also by Don Bluth), Chanticleer the rooster and his friends all live on a farm. But when all the other animals go to the city to find Chanticleer so they can get him back and stop the evil owl, instead of humans, all the inhabitants of said city are also animals! And also consider the fact that Edmund (the boy who was apparantly turned into a furry cat by the evil owl) and his parents are the supposed owners of Chanticleer's farm. On the surface this is easily explained by All Just a Dream, at least until the next scene where the live-action kid appears on the cartoon farm just to confuse the issue even more.
In Once Upon a Forest, when the three main characters get stuck in a storm drain we see a group of scary realistic rats scurry by before the tunnel gets flooded with water. One of the main characters is a cartoony wood mouse.
In Tom Sawyer, all the characters are anthropomorphic animals. At one point, Becky Thatcher mentions that baby kittens are some of her favorite things. She is a cat herself, and it's never made clear whether the kittens she is referring to are the equivalents of human babies or if there are non-anthropomorphic cats in that universe.
The entire cast of Kung Fu Panda are all anthropomorphic animals, but for some reason, the dragon statues are not anthropomorphosized.
Possibly justified, as the art style and architecture are based on Eastern styles, as fitting the nature of the film. The dragon statues shown are part of this, and one would assume that that world has the same or similar dragon legends as China or other Eastern cultures.
In Shark Tale, smaller fish serve as "humans", while larger fish serve as "transportation."
In Epic some of the animals (like Mub and Bufo) and plants (like the dandilions) can talk and interact like humans but others (like the mouse and birds) can only interact as animals of comparable size to humans would.
The American cut of Rock & Rule opens by saying that all the inhabitants of the future-North America are mutated cats, dogs, and rats, but later features a normal cat hissing and clawing at the camera when startled.
Tom and Jerry and The Wizard of Oz has Toto acting as a perfectly normal dog and farm animals acting like normal animals as well. This makes sense in the original film as only Oz has Talking Animals and Funny Animals... however the film features Tom and Jerry acting essentially like non-verbal humans. They are bipedal, are treated like farm hands, and apparently aren't pets. To make matters worse, Butch seems similarly anthropomorphic but lives in a dog-house and seems to be a pet.
For most of its existence, Alvin and the Chipmunks took place in what was basically the real world, just with three (later six) chipmunks who talked, acted like, and were the same size as human children. Then came The Chipmunk Adventure. In addition to the Chipmunks and Chipettes, the film contains non-anthropomorphic dogs, horses, lizards and sharks, cobras and alligators with slightly human traits, and... penguins that live in igloos, sleep in carved wooden beds, and carry lockets with photographs of their families. ...What?