The color of Columbus' hair changes back and forth between black and brown throughout the movie.
The ending implied that the land Columbus discovered will be known as New York City, yet on his first voyage to the new world he landed at The Bahamas, not near New York.
When Pico meets a Beaver after Christoper Columbus lands in the Bahamas, it is revealed that the North American Beavers live in the United States and Canada and can be found in northern Mexico.
The movie starts with narration by Mickey Rooney that helps explain the nature of 1492 Europe for any newcomers, before introducing Christopher Columbus and his goal to discover the New World. But as the movie drifts off into fictionalized characters exclusive to this version, the narrator doesn't come back at the end, and the characters are on their own in the long run.
The seagull's beak didn't move when he said "What's with him?".