- Celebrity Voice Actor: In the Japanese version, Professor Hale was voiced by veteran actor Naoto Takenaka.
- Creator Backlash: Takeshi Shudō was hospitalized during the making of the movie, and though he recovered, he didn't feel like going back to working on it, so he asked Hideki Sonoda to finish writing the story. Upon finding out the woman who shows up during the credits was supposed to be Molly's real mother, who was just in the hospital and not dead, Takeshi was outraged. He felt this went against the story he was originally writing. As a result, he never wrote another Pokémon movie after this.
- The Danza: Lisa Ortiz as Lisa.
- Executive Meddling: Takeshi Shudo's original script for the movie, about a T-Rex fossil on a rampage which also addressed the idea of real animals in the Pokémon world, was rejected; not for being too complicated, but because the suits thought, "A story where a bunch of minerals gain consciousness and comes to life won't be a hit."
- Name's the Same: Another Pokémon movie introduced a movie-only character named Lisa.
- The Other Darrin: The European Spanish dub of this movie, as well as Mewtwo Returns, does not keep the series cast; except for Ricardo Escobar as Tracey and Roberto Encias as Prof. Oak.
- What Could Have Been:
- The producers considered having Sean Connery voice Professor Hale in the English dub, but after the backlash after fans got over the fourth-wall jokes in the previous film, they decided against anything that might suck them out of the fictional world, including celebrity voices.
- An early script had an entirely different story addressing the question of, "What happened to real animals in the Pokemon world", in the form of the discovery of a fossilized Tyrannosaurus rex. Real animals would have been established to have existed (complete with photographs), yet no-one alive remembers seeing any. While the fossil is being studied, it comes to life and starts rampaging across the countryside, eventually hitting Pallet Town and Team Rocket's base, bringing the whole organization into the mix.
- Working Title: Prior to release, this movie was known both in Japanese and English (for some strange reason) as The Lord Of The Unknown Tower.
- Written for My Kids: Takeshi Shudō felt that the relationship between a father and a daughter is something the media too rarely portrays, and so wrote the movie with his daughter (who was born when he was 45) in mind, partly as a present for her (he was also concerned about his own health at the time). This made him all the angrier when the script was changed to have Mii/Molly's mother simply in the hospital, since his own mother had died in the hospital and he felt that it ruined the connection.
Trivia / Pokémon 3