** 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 its 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 were 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.
** Weirdly enough, the "Mewtwo's Origins" short, which is also the actual first 10-minute opening of the film, has yet to be released overseas passed its initial DVD release. It was dubbed into English, and they have every audio master to everything Pokemon that 4Kids dubbed, so re-inserting the segment with its dub wouldn't be that hard. It also makes some things in the film more clearer, like Mewtwo's characterization, why his Charizard, Venusaur, and Blastoise have weird markings on them, and ''why'' he came into creation in the first place. The film flows better with it, so not at least including it as at least a bonus feature for the later releases is baffling.
* RetroactiveRecognition: Creator/BilliePiper (credited simply as Billie) sings one of the end credits songs, "I'm Makin' My Way (Any Way That I Can)."
* 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 originals are the real things. They won't lose to the copies if it comes down to a fight in which neither side uses any of their special powers.
*** Granted the actual dialogue still implies that Mew's opinion on the clones was a little low.
** I'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.
** It is commonly believed that the movie was originally meant to be the finale of the series before the anime was renewed, due to the Japanese teaser trailer having scenes that aren't in the movie. However, the anime was renewed before the film even entered pre-production, and it was never actually intended as anything more than a side story.
* UnintentionalPeriodPiece: The English dub's soundtrack is a nice little time capsule of late 90s bubblegum pop.
** [[http://www.dailymotion.com/video/x4pmwla The Japanese teaser trailer]] consists entirely of scenes from an earlier draft of the movie.
** [[http://www.style.fm/as/05_column/shudo166.shtml One of Takeshi Shudo's blogs]] revealed that there would have been an animé episode prior to the movie where Ash and Mewtwo crossed paths, but the four-month hiatus brought on by the "Electric Soldier Porygon" incident put an end to that.
** Mew could originally speak like Mewtwo could, but director Kunihiko Yuyama figured Mew flying around wordlessly would be more impactful than it "droning to Mewtwo about the meaning of life", thus all its dialogue was replaced with, "[[PokemonSpeak Mew]]".
** The scene of Ash saving Pikachu from the cloning machine wasn't originally present, but was added by Yuyama, who believed the film didn't have enough action scenes.
** According to Rachael Lillis, Warner Bros briefly considered replacing the entire voice cast with celebs, and even made an offer to Creator/LeonardoDiCaprio to voice Ash.