Factual error: In "Pikachu and Pichu," when Pikachu and the Pichu brothers come to the big play structure thing, there are a bunch of Pokemon around, including a red-and-white, ball-shaped Pokemon called Voltorb. The dubbers for the English version made a very noticeable error here: instead of Voltorb saying "Voltorb," (almost all Pokemon say parts of their names when they speak) it says "Electrode," which is the name of a similar-looking, but different Pokemon. The two are both red and white, but the difference is that Voltorb has eyes on the red part of its body, while Electrode has eyes on the white part of its body.
Continuity mistake: During her battle with Ash, Lisa jumps over a patch of flowers and sends out her Girafarig. During this shot, the flowers are considerably higher than the fence that surrounds them. However, a few shots later, the flowers are seen again, but this time they seem to be lower than the same fence.
Trivia: In the original Japanese trailer, most of the scenes were fully animated, yet not used in the final cut. Some of the shots were Ash standing on top of a crystal pillar, as the camera pans around him and he is searching for something, a bunch of random wild Pokémon running away from the crystallization, and a shot of Mewtwo standing at the entrance of a cave with lightning cracking behind it. Supposedly, the 3rd and 4th movies were to inter-connect, with Mewtwo being the one who connects them. Perhaps the anime producers decided to throw that away and instead advertise the then-new Pokémon Crystal game? After all, several elements from the game (the Unown, Suicune, Celebi) appeared in both movies.
Trivia: Much like Movie 2, the Japanese version has two titles. "Emperor of the Crystal Tower" was written in Kanji, but "Lord of the Unknown Tower" is written in English. The second title was used as the English Version title in the original trailers, but was changed to "Spell of the Unown" so as to not offend any religious groups. Also, the mini-movie's title is similar. The Japanese one is "Pichu & Pikachu" while the English one is "Pikachu & Pichu."