Dr. Dolittle's tongue changes color in opening scene with stray dogs.
When Dr. Dolittle visits the "God Beaver", it offers him a fish from its store. Beavers are herbivores, they don't eat fish.
Sonny (Archie's rival) is said to be a Kodiak bear but said species is exclusive to Alaska and wouldn't be roaming around a forest in California.
The deer speaks with a female voice, yet has antlers and is therefore a male.
A bee with a male voice yells, "defend the hive!" and a chorus of bees yells "attack!". Male bees never leave the hive and don't have stingers. The same mistake was made in Bee Movie (2007).
The animal referred to as a weasel in the movie is actually a ferret, a completely different species.
Grizzly bears have been extinct in California since the 1920s.
When Dolittle is speaking to the dog in the meeting and asks did any dogs do security? Watch the dog licking himself because what Dolittle says next about licking doesn't match his mouth movements meaning Eddie probably said a word that sounded like a swear that was covered up.
When Doctor Dolittle is visiting Crocodile Hunter Steve Irwin's TV set in Australia, the animal is presented as an alligator (which it is) but there are only crocodiles in Australia. To add insult to injury, the alligator has an Australian accent.
John calls an opossum a rodent. It is a marsupial.