Bad Export for You: When the triple-film DVD came out in 2009, many expected all three movies, including this one, to be widescreen unlike the previous VHS and DVD release. Sadly...no dice.
Hey, It's That Voice!: Mewtwo's Japanese voice actor, Masachika Ichimura, once played Eric in the stage adaption of The Phantom of the Opera. That's right, Japanese Mewtwo is The Phantom.
Urban Legend of Zelda: There's a rumor circling that Mew in the Japanese version said that the originals were inferior and should perish. According to Nyarth it's dialogue was:
The real one is real. If they fight only using bodies without skills, the true ones will not be beaten by their copies.
What Could Have Been: This film was originally going to serve as the finale to the series, but then the series was renewed and the whole film was rewritten. The Japanese teaser trailer shows clips from the original planned film.