Revealing mistake: At the end, when the NYC children are rushing toward the peach to scoop out a piece to eat, you can see one little girl running with a piece of peach already in her hand.
Plot hole: Why is that shark machine even there? The only reason it's there is to help the plot, and I don't see how it is of use to anyone in the corporate world. If the shark just ejects the fish it turns into fish heads out to sea, there is too much chance they will be ruined by carnivorous fish or weather before they are picked up. And fishing companies should know better.
Trivia: While Centipede is on the skeleton ship, he enters into a room where the Skeleton Captain is laying on a compass, and Centipede murmurs, "A Skelington?" This was probably a reference to a previous Tim Burton character, Jack Skelington in "The Nightmare Before Christmas". The fact that the Captain greatly resembles Jack supports this theory.