Goofs

When we first see Gmork (the wolf) in his cave (at around 5 mins), his teeth are close together and short but when we see him talk to Atreyu (at around 1h 12 mins), his teeth are now further apart and longer.

When Falkor first appears, he flies in a distinctive undulating motion, like an otter swims through water. For the rest of the movie he flies in a straight rigid line, with or without a passenger on his back.

The knight's staff lands on the right Sphinx's foot once he falls off his horse, but later on when Atreyu is attempting to cross the gate, the knight's staff is laying parallel to the knight's dead body.

After Atreyu falls off Falkor, he wakes up by the ocean with his feet in the surf. It then cuts to a longer shot that shows him several feet away from the surf.

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.

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.)

Atreyu still has 109 miles to go before he's at the Southern Oracle, but it doesn't seem that far. It is probable that the two gates he passed through transported him much closer to the Oracle, given how powerful they were.

In the scene where Falcor delivers Atreyu to Engywook & Urgl, Atreyu is clearly much larger than the small, old couple. Later, when Engywook and Urgl are standing on/near Falcor they they are about the same size as Atreyu in relation to Falcor.

After Atreyu talks to the Rockbiter on the beach, the spot where the ground will crack is visible before the ground cracks.

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.

When Bastian is being forced into the garbage bin by the bullies, he wraps an arm around the rim and pulls himself up, making it obvious he is actually getting in on purpose.

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.

As Atreyu speaks to the sphinxes of the Southern Oracle huge pieces of their faces crumble and break off. As he runs away we see their faces completely intact.

In the trailer, the name of the old elf is given as Inglenook, but in the film his name is Engywook, which appears also in the subtitles.

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.

When Bastian's Father gets the blender ready, a crew member is seen moving, reflected off the microwave oven.