Producers and the director, Michael Haigney stated that there was a lot of trouble having to match the animated lip movements. The script was written twice to try and make sure that all the dialog matched up. They also said that they were very happy that Mewtwo was a psychic Pokémon, because he would converse using his ability and so there were not many times where his mouth was moving, so they did not have to work around making the dialog match his mouth movements.
When Brock states that he didn't know vikings still existed, Ash says they usually live in Minnesota. This is obviously a reference to the Minnesota Vikings football team. But in some dubs, this joke isn't used.
In Japan, the main character (Ash) is known as Satoshi, while his main rival (Gary) is known as Shigeru. These Japanese names were taken from two game designers :- Satoshi Tajiri (original creator of Pokemon) and Shigeru Miyamoto (one of the head game designers at Nintendo Co. Ltd) who are in reality good friends. it was Miyamoto who pushed Tajiri's ideas to Nintendo CEOs and got the Pokemon game franchise started.
The original Japanese version of the movie had a different musical soundtrack with almost no vocal songs, and many scenes that do not feature any music at all. When this film was dubbed into English, the music was also re-scored and was also added to the scenes that originally had silence in them.
A narrator and Mewtwo's voice were added in the American version, in the first segment of the movie, to help better explain the movie to people who may not have had such a wide knowledge of the Pokemon craze, for example parents who took their children to see the movie.
When Mewtwo is shown defeating Arcanine and Nidoking, we see a shot from behind and we see the back of the trainer. In the commentary it is told that this trainer is Gary, Ash's rival from the series. They then go on to joke about his 'cameo', saying that Gary's agent wouldn't let them show his face, and that Gary is actually a stand-in in that shot.
Originally slated for a November 12 release date, but the date was pushed ahead to November 10 to take advantage of the long weekend. Many posters for the movie out there still have the inaccurate Nov. 12 release date on them.
The original Japanese story showed Mewtwo in a more favorable light, as feeling that it has no place in the world and so wants to "earn" its place. The English dub opted to just make Mewtwo an emotionless tyrant who wants to destroy the world, a decision that both fans and critics criticized. In hindsight, the producers felt they made the wrong decision.
When the film was first conceived, in 1997, it was planned to be the series finale of the Pokemon TV show. However, the phenomenal reception to the show resulted in minor changes of the movie so that it would hint that the series was not yet over. In addition, it was released in theaters in-between major episodes of the show, rather than the television finale as was the original plan. (The infamous Porygon incident also contributed to this.)
The trivia item below may give away important plot points.
The "tears of life" concept comes from Norse Mythology. In Norse Mythology the god Baldr was killed by his brother Hödr. Odin sent his son Hermondr to Helheim (the world of the dead) to ask his niece Hel, the goddess of death, to let Baldr come back from the dead. Hel said that if the whole cried she would return Baldr. Unlike this movie, the legend did not end happily. This reference is possibly a reason for the use of viking-disguises for Team Rocket.