Audio problem: About halfway through the movie, Richard and Fantasy reunite on the island. Richard says, "Fantasy." and Fantasy responds with, "Well, what were you expecting honey? The tooth fairy?" When she says "the tooth fairy" her lips are saying something completely different (and it's even worse, since it's a close-up of her face).
Continuity mistake: Throughout the entire movie, the irregularly-sized characters are constantly changing size when compared to one-another. Except for Barky (even Junior, he is awfully big for a baby) I.E. when Bastian accidentally steps on the gnomes' house, the gnomes are the height of Bastian's shoe, yet when they run out of the house, they are as tall as his leg up to his knee cap.
Continuity mistake: During his monolog in the scene on the airplane, Briggs introduces Wayne as a private but, in the next scene when they wash up on shore Briggs addresses Wayne as lieutenant.
Continuity mistake: When Cane's agent gets out off the bookstore and crosses the street, the cars keeps changing all the time between shots.