Revealing mistake: In several scenes, it is obvious that the animal actor playing Bagheera is actually a black jaguar. For example, the jaguar is larger and heavier than the leopard/panther. The scene where Bagheera tackles a poacher, he is much to large and heavy to be a leopard/panther.
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: When Meo and 16 are competing with weapons, 16 has a staff but when he bows to grand master he has 2 swords in his hand.
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: Norby rips a bit of Veeko's pants from the right leg; when we see a close-up of Pantoliano, the filament popping in frame from above comes from the left side (if it's a shoelace and not part of the torn pants, Veeko's boots were not unlaced). As he falls, we see for a moment Veeko's feet and there's no torn fabric dangling. (01:13:50)
Revealing mistake: When the tiles pop off the wall near the beginning, each pops off right in the middle. The nozzles squirting out the water are obvious.
Visible crew/equipment: After the little girl leaves the grocery store with Dodger, the monkey, the overhead microphone can be seen above her head.