When Bastian stands in front of the monster spraying it in the face with a spray can, you see Bastian stretching as far as he can, but he still can't reach any further up than the monster's chest. In the next shot, Bastian's hand is in the monster's face.
The dark leather cord holding Auryn around Bastian's neck suddenly turns into a gold chain half way thru the movie.
Mr. Koreander's name begins with a K in the credits as well as on the window of his bookstore, but as Bastian's father reads in the car, we see that it begins with a C within the text of The Neverending Story.
When Bastian and Atreyu are sitting by the fireplace, Atreyu puts his arrow on the ground. In the close-up he has the arrow in his hand again.
When Bastian is lying in his bed, he is looking at a picture which stands at the edge of his night table. In the next shot, the picture has moved in on the table.
Each time Bastian wishes for something using the Auryn, a lost memory comes out of the Memory Machine as a marble. In the beaker, there are a lot more of those memory marbles than the 33 memories Bastian wished away. He may have made more wishes elsewhere in between the time that he is shown.
When the Rockbiter eats the rock Junior gave him, it breaks and has glass shattering with dust pouring out. The composition of the rocks in a fairy-tale land may not be the same as the known minerals of Earth.
When Bastian puts on the invisibility belt for the second time, it's obviously recycled footage from the first time he used it. His motions and expressions are exactly the same.
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.
When Nimbly lands on the ship, the wires that are holding him are visible.
When the last monster sinks into the ground a black mat covering the hole in the ground is visible.
When Tri-face is introducing his memory machine and his three faces are rotating, we can see where the camera shot changes to show the actor.
When Bastian puts Auryn under his shirt, there's a metal against metal sound, yet Bastian isn't wearing any metal.
The face of a man wearing sunglasses is reflected in the microwave when Bastian is getting the food out.
Mr. Koreander's shop is stated on the label to be located in De Forest, a city in Washington State. In multiple city scenes, there are Canadian references, such as a taxicab with British Columbia plates, a Canadian flag, a Canada Trust sign, a Bank of Montreal sign, and a sign mentioning Vancouver. Bastian's father's car also has a Washington D.C. license plate instead of a Washington State license plate.
When Bastian's father is stopped in the road, you can see that his car has a Washington DC license plate even though they are supposed to be living in Washington State.
In this movie, Bastian has a fear of heights which includes him having to dive off a 20-foot diving board, but in the first movie, Bastian is flying on Falkor's back miles up in the clouds.
Bastian is given the ability to wish for anything. Yet, either wastes it on silly things ("a spray-can"), or doesn't wish at all. Even in life or death situations, he hesitates to make a wish. The reason for this is never given. Even when it's explained he loses a memory with each wish, Bastian himself doesn't know this at first. So there is virtually no reason for him to not be wishing for anything.