Other mistake: In the intro to the Pastoral Symphony, the narrator identifies the deity who cloaks the world with Night to be Morpheus, who is the Greek god of sleep and dreams. However, the character in the animation is fairly obviously female, with long hair, eye shadow, and lipstick. My theory is that the character was intended by the art team to be Nyx, the Greek goddess of Night. Night would be a more likely candidate to be making it nighttime across the world, while Morpheus would be more likely to put people to sleep or send them dreams.
Suggested correction: Without further evidence/proof, this theory remains just that. A theory.
Other mistake: On the first morning at Manderlay, as the girl is leaving the dining room, she slips and nearly falls but Frith is there to catch her, but Frith was way into the dining room; there is no way he could have been close enough to catch her.
Other mistake: Chapter 2: Freezing Torture. When a Ming ship launches the first bomb at Flash and his friends, you can see somebody walking or skiing toward the explosion. The problem is that they are not moving. It may be footage from another film.
Other mistake: Noah, the brother, just disappears from the movie with no explanation at all.
Other mistake: When Gepetto paints Pinocchio's smile on, he uses a darker red. But the smile is in black.
Other mistake: In the windmill scene, the windmill reverses directions twice to signal the airplane. However when Joel McRae enters the windmill and we see the machinery it is obvious that there is no mechanism to reverse the windmill against the wind.
Other mistake: It's the Professor's 60th birthday and the candles on his cake must be the trick type - they keep going out as the cake is carried into the room, but they quickly come back on again. But when it comes time for the Professor to blow them out, there's no problem - he blows them out easily.