Box Office Bomb: The second and third movies in the U.S. For The Next Chapter, Budget, $36 million. Box office, $17 million (domestic), $56,468,971 (worldwide). This led to the third unrelated film having a budget of $17 million. Box office, $5 million in Germany, but allegedly not even 5 figures in the States, where it screened in limited release, was ripped to shreds, and eventually came Direct-to-Video without Warner's involvement (Disney/Miramax distributed it instead).
Dawson Casting: The "high school students" in III are in their mid-20's - or older. Similarly, Julie Cox is cast as the "Childlike" Empress despite being 21 by the time the film came out, which is noticeable in that she was actually taller than Jason James Richter, who played Bastian in that film.
Disowned Adaptation: Michael Ende filed an injunction to stop the production of the film, or failing that prevent them from using the title of his novel. He was unsuccessful, and demanded that his name be removed from the credits.
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.
Executive Meddling: After the first film's test screenings revealed that audiences were not enthused with Klaus Doldinger's score, the studio commissioned Giorgio Moroder to replace some of the original music with his own. Wolfgang Petersen was not pleased, though some could be argue that Tropes Are Not Bad because of the title song, one of the most memorable aspects of the film to many viewers.
Franchise Killer: The third film thanks to actually being considered worse than Chapter 2 (which only scored a 14% on Rotten Tomatoes). Characters didn't retain their original personalities, Atreyu being absent and the series' iconic theme song at the end of the movie (which reused a "Born to Be Wild" rendition) were the final nails in this film's bookcover.
The Other Darrin: The second movie has only one of the main actors from the first movie, and the third movie doesn't have any of them.
Playing Against Type: Jack Black, who is typically known for plying somewhat bumbling yet lovable misfits, is the Big Bad of the third film.
Troubled Production: As the most expensive movie made in Germany up to that time (and, indeed, the most expensive movie made outside the US or USSR at that time), it's hardly surprising that a bit of this trope was responsible for that:
Poor Noah Hathaway. Right before production was to begin he suffered crushed vertebra in a horse-riding accident, putting him flat on his back in a hospital bed for two months while he recovered. Then the green-skinned look Atreyu has in the book had to be scrapped when it made him "look like fungi" in screen tests. Lastly he was caught underwater during the Swamp of Sadness scenes and lost consciousness before he could be rescued. After the near-blinding noted under Enforced Method Acting, Pedersen decided not to shoot another take due to the risk of further injury to his already battered actor.
Tami Stronach, the Childlike Empress, also got into the injury act, losing her two front teeth shortly before filming started. It took her some time to get used to the hastily-made bridges; in some scenes they left her with an audible lisp.
The scenes in the Swamp of Sadness cost $130,000 per day of filming for the two months it took to film those scenes. This led to two other special-effects scenes being canceled due to financial reasons. One of which, the first appearance of Falcor, left some plot holes as a result.
Ende, as noted under Disowned Adaptation, hated the movie and sued unsucessfully to have either the whole production shut down or the title changed. He particularly took issue with the film's ending, which shows Fantasia restored with little creative input from Bastian and also shows Falkor crossing into the real world (noted to be impossible in the novel, as Fantasticans who enter the real world become lies). This is why Ende's name is not referenced in the film's opening credits.
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.