Factual error: Raphael tells Yoshi that being a kid, he shouldn't think about war but rather fly "one of those things." He is pointing at kites who have artwork (kabuki-ish makeup with the modern japanese flag) that looks out of place for 1603. (00:56:40)
Factual error: The movie is set in New York, and Rocks is fighting wolves. Wolves are no longer found in New York.