Other mistake: At the end of the movie when some of the pods are being activated, there are two orange ones with the same number.
Other mistake: As they're chasing the giant fish and the ship is bouncing on the waves, we can see in some shots a major design flaw - the ship has no rudder.
Other mistake: At the end of the film, as Kenai walks up to Koda after he's been transformed back into a bear, Koda leaps on him in joy. If you look closely at Kenai's hind legs, there are a few frames of animation missing. His legs go from a standing to a sitting position instantly. It's barely noticeable (no pun intended).
Other mistake: During the scene at the beginning of the movie where Taro Kitano and Vert Wheeler are racing around the desert, as Taro slides around the corner, his front wheel clips through his fender. (00:06:59)
Other mistake: When first showing the Hoenn Pokémon League, the match is about to begin, but the screens for it are off. (00:00:56)