Continuity mistake: When Atreyu and Bastian is sitting by the fire you see Atreyu holding an arrow in his left hand when he is getting up. When it cuts the arrow is in his right hand. (00:36:25)
Character mistake: The spelling of Koreander/Coriander's name varies between the opening credits (spelled with a C), the shop window (spelled with a K), the inner cover of the book (spelled with a K) and the book's text (spelled with a C).
Revealing mistake: When Falkor is talking with Atreyu and says "Bastian is losing himself with every wish," you can see that Falkor hasn't got any body. (01:01:00)
Continuity mistake: When Bastian stabs the toast and lifts it up you can see a big chunk of meat hanging out of the toast. When it cuts to a closeup of the toast the chunk is gone. (00:02:20)
Revealing mistake: When Atreyu lies dead, right before Bastian awakens him, you can see his neck pulsate. (01:12:20)
Continuity mistake: When Bastian and Falcor fly out the gates of The Silver City, the gate closes in the same position three times. (00:27:15)
Continuity mistake: When Bastian grabs the roll of paper he pulls some paper over the kitchen bench. When it cuts, the paper is rolled back. (00:02:40)
Continuity mistake: When Bastian gets into Koreander's book store you can see a stack of books lying next to a huge book. Later when we see the stack with the 'Neverending story' book on top, the formation of the stack has changed. (00:08:50)
Revealing mistake: When the ground around the empress' castle is tearing apart you can see a tree falling down. However you can also see the wire pulling it down. (01:08:00)
Visible crew/equipment: When Nimbly lands on the ship, the wires that is holding him are visible. (00:15:15)
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. (00:28:40)
Continuity mistake: When one of the monsters comes up from the ground it is coming up right in front of Bastian. When it cuts, there are suddenly two monsters in front of Bastian, and the hole in the ground the monster came up from is gone. (00:18:50)
Continuity mistake: When Bastian is lying in his bed, he is looking at a picture which stands at the edge of his night table. When it cuts the picture has moved in on the table. (00:07:35)