Disowned Adaptation: Michael Ende requested that the movie be killed before release or, failing that, not be associated with his name in any way. They did neither.
Enforced Method Acting: That look of shock on Atreyu's face and how dazed he looks getting up after he kills Gmork? That was real. Apparently, they didn't realize how heavy the mechanical wolf puppet could be, and when they shot the scene, it almost knocked out Atreyu's actor. They decided not to try for a second shot after he revealed the claws almost poked out one of his eyes too.
The Other Darrin: The second movie has only one of the main actors. The third has a lot of new actors.
Vaporware: German game developer Discreet Monsters' The Real Neverending Story, which wasn't really getting anywhere even before Discreet Monsters was felled by the end of a tech bubble. The main personnel involved eventually produced a much less ambitious game, Auryn Quest.