Revealing mistake: Right after Atreyu discovers that Xayide is stealing Bastian's memories we see Atreyu and Falcor sitting on a cliff with an entire landscape in the background. It is easy to see the whole thing is fake, cause the camping place which they sit on shimmer and moves. The camping scene has been shot earlier and is now placed on a fake background, and someone is adjusting the picture.
Revealing mistake: When the dragon is flying by the castle, the castle is shooting a laser at it as it flies by. Then the dragon explodes just as it flies out of camera angle. However it is that the explosion comes from the ground down by the edge of the castle, and not in the air where the dragon is flying.