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: When the two kidnappers realise the baby is drooling on them from the skylight, Mantegna in the shot from above is holding the pen in his right hand. It was in his left a moment earlier. (00:25:10)
Continuity mistake: When Ernest is messing with the pipe in the locker room the toilet seat in the middle stall goes from being up to down and back up again.