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: In the boat chase, the distance between the boat and the jet skis keeps changing between shots.
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: In the scene where the wagon train is waiting for Wagonmaster Harlow to decide which fork in the road to take, all the shadows are to the left. As they approach Harlow, the shadows are in front and moment later when the wagons move off the shadows are to the right. (00:26:20)