* AbsenteeActor: Ash's Pidgeotto is nowhere to be seen in the main film and is the only member of Ash's team at the time to be absent from the fight. This was probably to avoid confusion with Corey's Pidgeot. It does appear a few times in the short film preceding the movie, though.
** 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. This was later remedied with the triple feature Blu-ray release in 2016, though the releases add problems of their own, as detailed in the note in the KeepCirculatingTheTapes entry below.
** No Western DVD release has included the Japanese version. This is par for the course for ''Pokémon'', but the Japanese version of this movie is in greater demand than the other movies due to its differences from the English version.
* CowboyBebopAtHisComputer: Mew was, at least for a short period, mistakenly referred to as Mewtwo's mother rather than it's clone counterpart. This also ignores the franchise's (mostly) strict adherence to gendering Pokémon.
** This film as well as the latter two movies took years to get a Blu-ray disc release thanks to years of disputes between Warner Bros. (the licensees of the movies for all territories except Japan), The Pokemon Company, Nintendo and Toho. By TheNewTens, fans we're getting irritated over having to deal with the 4:3 aspect ratio of the DVD and VHS releases and pushed for the disputes to end so they could get the films remastered for high definition. The disputes were finally resolved in December 2015, and a Blu-ray disc release of all three movies in a triple-feature Steelbook pack was announced for release in February 2016, in time for the ''Pokémon'' franchise's [[MilestoneCelebration twentieth anniversary]]![[note]]Though there are a couple of catches: First, the films will be presented ''only'' with the 4Kids English dubs in 2.0 lossy stereo sound, and second, all of the special features from the [=DVDs=] will not be available in the set, meaning no Pikachu shorts at the beginning, either[[/note]]
** The 1998 theatrical version of the film has remained under this status since the release of the ''kanzenban'' version a year later. The latter version [[GeorgeLucasAlteredVersion re-does a large number of shots in the film to add in CGI]] (be it replacing entire effects such as whirling clouds or simple choreographic retouches); this is the version that would be used for the film's English dub and all following home video releases. The theatrical version, meanwhile, has never seen a single re-release since its initial VHS & [=LaserDisc=] pressings in the first half of 1999, and only continues to survive thanks to the likes of [=eBay=], Amazon, and a small number of video-sharing sites in the most obscure corners of the internet.
* ThrowItIn: The commentary remarked that Misty's "please, no" reaction to [[spoiler:Ash's death]] was originally, jokingly ad-libbed by Rachael Lillis as [[CallBack "My bike!"]] when trying to find a workable two-syllable reaction to said event.
** There's a rumor circling that Mew in the Japanese version said that the clones were inferior and should perish. According to Meowth (Nyarth in this version) its 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.
** Granted the actual dialogue still implies that Mew's opinion on the clones was more than a little low.
** Recently, it's been revealed that [[http://www.behindthevoiceactors.com/forums/showthread.php?t=13970 the reports of the death of Mewtwo's original VA]] [[Creator/MarkTwain have been]] [[ReportsOfMyDeathWereGreatlyExaggerated greatly exaggerated]].
*** And he apparently voiced Mr. Fuji as well, instead of Creator/MaddieBlaustein.
* UnintentionalPeriodPiece: The English dub's soundtrack is a nice little time capsule of late 90s bubblegum pop.
* WhatCouldHaveBeen: 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. [[http://www.youtube.com/watch?v=b70GRNYnacI The Japanese teaser trailer]] shows clips from the original planned film.