Continuity: Sand on Atreyu's chest when washed up on the beach.
Continuity: After Atreyu leaves Rockbiter, a large wall of rocks is (not) there.
Revealing mistakes: Support stick for asteroid masks verticals section.
Crew or equipment visible: When a sleeping Atreyu is nudged awake by his horse, Artax, a sugar cube can be seen falling out of the shot. It is only visible in one frame as white under his left sleeve at 28:39 on the DVD.
Continuity: In the US version, when The Nothing first appears and Rockbiter drives away, his position relative to the camera changes inconsistently between shots.
Continuity: Toward the end of the movie while she is speaking with Atreyu, the middle two rows of beads in the head piece that the child-like empress is wearing, change position between closer together and further apart from 81:00 to 85:00 on the DVD.
Revealing mistakes: When Morla sneezes for the first time, the camera switches to Atreyu and you can see a clear image of the stuntman who does the actual falling at 37:56 on the DVD.
Revealing mistakes: In the wide shot from 50:53 to 50:57 on the DVD where Atreyu scales the mountain to look through the telescope at the first oracle, you can see a horizontal line where the set wall (lighter blue) and ceiling (darker blue) meet. Basically, you can see that they are in a room instead of out in the desert.
Continuity: When Bastien and his father are talking at breakfast his father drinks about half of his egg drink before sitting down, later when he picks it back up again the cup is about three quarters full again.
Continuity: A Z-shaped reflection can be seen floating around the left side of the picture as Bastian is on Falkor's back pointing out Atreyu on the ground.
Revealing mistakes: When the Night Hob reaches the Ivory Tower he is seen pulling himself up through a gap in the Tower. His Bat appears via an adjacent gap. They are meant to be at the top of the Tower, and yet behind them is a visible blue screen, not clouds nor the sunset.
Incorrectly regarded as goofs: When Atreyu is in the Swamps of Sadness with his horse, the horse sinks because it gives into the sadness, but Atreyu doesn't sink, even though he is crying and sad that his friend has died. Though not properly shown in the movie, the book explains how AURYN is protecting him. (His eventual near-sinking at the end of the scene, which never occurred in the book, is due to the plot changes that were made for the movie.)