Deliberate mistake: The balloon llama the chipmunk makes has legs which are completely detached. The pairs of legs should be twisted together. Without this, it looks like the balloon has 6 different ends.
Deliberate mistake: You might be wondering where Terry suddenly comes up with Jolly Jack all of the sudden after escaping the lab. In the commentary, they say that the Joker, in his transmission to Terry in the lab, was supposed to be eating out of a candy jar with "Jolly Jack" on it, but couldn't have it due to time constraints.
Deliberate mistake: Some of the text in this movie is in English, but some is in Japanese. Most noticeable when Tai writes the letter to Sora.