•The Princess and the Frog has Naveen and Tiana turned into frogs. Naveen is larger and rather dull in colour whereas Tiana is smaller, cuter and more brightly coloured. Unless they're supposed to be bullfrogs or something of the like, Tiana should have been the big one.
•Finding Nemo is apparantly about a father clownfish's journey to rescue his kidnapped son, Nemo. According to the film's prologue, the father clownfish is constantly worried about his son's survival because of his wife and all the other eggs being killed by a barracuda. In real life, all clownfish are born male, but turn female if the dominant female dies.
Averted in Kung Fu Panda 2, where Po and the Furious Five square off against a sickly, albino male peacock who wants to destroy Kung Fu forever. When said peacock's mother is shown (in shadow puppet form), she clearly doesn't have a train.
Played with, and played straight, in Bee Movie. One scene involves Barry mentioning that the queen of one of the artificial hives being used to harvest honey for humans is a male bee crossdressing up as a woman. • For that matter, all the bees in the hive are worker bees. In reality, only sterile female bees are workers; there is a queen whose only job is to lay eggs, and drones (male bees) exist only to mate with the queen and then die.
It also features a male mosquito who drinks blood.
Barnyard is infamous for this as it has a level of confusion somewhere between bizarre and Squick. Its hero is a male cow—not a male cattle or a bull. He has udders. And at the end, his girlfriend has a calf, and he clearly says it's a boy, even though the kid's got udders too. What makes all this REALLY odd.
In Madagascar the lemurs are lead by King Julien. Lemurs in real life are matriarchal.
Mr. Twitches from Tinkerbell and The Great Fairy Rescue is a male calico cat. Tortoiseshell and calico cats are usually female.
Perhaps parodied on Phineas and Ferb, which occasionally brings up the idea that Perry the Platypus could lay an egg. Nobody ever seems to realize that he's a male platypus.
Played straight when Perry and Candace switch bodies, Candace somehow can sweat milk, something that female platypi do.
...Note though that she's in Perry's body... who is said to be male. That means that either their genders somehow switched when their minds switched (not unreasonable for this show) or that the Flynn-Fletchers need to change veterinarians. However, that second theory does raise the question of why Perry is going along with the misunderstanding with his boss and his nemesis...
Giving some credence to the former theory is the fact that a later episode shows that Perry has venomous ankle barbs, something only male platypi have.