Corrected entry: Early in the film, Ash defeats a Golem using one of Pikachu's electrical attacks. Electrical attacks can never harm a Golem, no matter how much stronger the electrical Pokemon is.
Corrected entry: When Mewtwo collects the trainer's Pokemon in the special cloning balls to be cloned, he takes away Ash's Charizard. Why would Mewtwo take away Charizard to be cloned? He already has a clone of Charizard so he wouldn't need another one.
Correction: Then why doesn't the cloning machine clone another Charizard? If the cloning ball with Charizard went down to the cloning machine then surely that Pokémon would have been cloned.
Corrected entry: Misty is shown with one set of Pokémon in one shot and with some entirely different ones in another.
Correction: Please elaborate more. At this point in the series, Misty's lineup is Togepi, Staryu, Goldeen, and Psyduck. All of them appear in the mini-movie, but none of the Pokémon ever appear on-screen with their Trainers (aside from Pikachu). During the main feature, Misty calls Staryu to rescue her from the storm, then calls Psyduck out after arriving to New Island (Togepi hides in Misty's bag for most of the movie). If you're referring to any event after Mewtwo reveals his grand scheme, then that can be explained as the chaos getting out of hand and the Pokémon running for cover.
Corrected entry: How come the superclone Wigglytuff said 'gogoba' at the end? It's not supposed to do that.
Correction: It actually does say "Wigglytuff". The closed caption puts it up as "gogoba" for some odd reason. It's not an actual movie mistake, just a mistake in the captioning and/or subtitles.
Corrected entry: Nurse Joy (under the control of Mewtwo) tells Ash and company to bring out all of their Pokémon. So where are Pidgeotto, Onix, Geodude, Zubat, Staryu, and Goldeen? They were never brought out.
Correction: Nurse Joy never actually said to bring out ALL of their Pokemon. She says "Please release your Pokemon from their PokeBalls and join the others." I don't know why they didn't release all of their Pokemon, but they were never told to release them all.
Corrected entry: The male trainer with the Gyrados claims all his Pokemon are water types. When he introduces his team, a Nidoqueen is there. Although Nidoqueen can learn water attacks, its classified as a Poison/Ground type.
Correction: A lot of trainers do that. If the majority of their Pokemon are one type, they tend to say ALL their Pokemon are that type. Like Misty. She has a Togepi, but she says ALL her Pokemon are Water-types. Another explanation would be that this trainer counts his Nidoqueen as a Water-type because it knows Water attacks.
Corrected entry: When Mew appears for the first time, someone shouts Mew. It appears to be Prof. Oak's voice, but Oak isn't anywhere NEAR New Island. So, why would we hear him talk?
Correction: Anyone could sound like him. I got the feeling that it was 'dexter' the voice of the 'pokédex' (or more properly pokémon zukan).
Corrected entry: In Pikachu's Vacation, after the song has finished, all the Pokemon run towards the park, knocking Pikachu over. The last Pokemon to go past is Psyduck, who steps on Pikachu's head. We then move over to Togepi, with Squirtle, Bulbasaur, and, strangely, Psyduck. I thought he was in the park?
Corrected entry: During the introduction, there are two visual mistakes with the trainer's Venomoth: 1: The three horns on its head are all about the same size; the middle horn is meant to be at least twice the size of the other two. 2: The color of Venomoth's eyes are white; they are meant to be blue.
Correction: No two Pokemon are exactly the same. It's possible that this trainer's Venomoth is from a different area, like the Orange Islands or the Johto/Hoenn Region.
Corrected entry: In the scene where trainers are flying to new Island, a boy on a Pidgeot takes off. A few frames later, and Officer Jenny appears. We then see him take off again, except this time on a different Pokemon, a Fearow.
Correction: The person on the pidgeot is different to the person to the person on the fearow. The person on the fearow did not make it to new island. This is discussed in the audio commentary.
Corrected entry: When Charizard gets his head stuck in the short before the movie, Pikachu's Vacation, if it goes into the play thing with holes with no problem, why won't it come out easily?
Correction: Because Charizard head is shaped sort of like an plastic plug, so when it's inserted there is no problem but when he tries to take out the head, the backside of Charizards head "expands" like a plastic plug and making it almost impossible for him to take out his head.
Corrected entry: There was actually supposed to be a bit added on to the start of the movie explaining how Mewtwo could talk and everything, but was cut in the actual movie. Apparantly Mewtwo was raised by a geneticist's cloned daughter who taught him everything, but she died. Mewtwo was angry at humans for taking it friend away and then the movie continues in similar fashion to what we're used to.
Correction: Actually, Mewtwo's Origin was NOT at the start of the movie in theaters in Japan. In Japan, it was a bonus extra, just like it is in the U.S. And judging by the animation during the second half of the story, it was animated for the Mewtwo TV Special ("Mewtwo's Return" here in the U.S.) and not for the original movie. (The movie part has the same animation as MSB, but the part with Amber & Mewtwo has the same animation as the special.)
Corrected entry: During the opening theme song, the "pirate" trainer that challenges Ash at the end of the battle throws five or six Pokeballs. Of those six, four hit the ground and release Pokemon and of those four Pokeballs only three Pokemon show up. Where did all the Pokemon go?
Correction: The trainer only throws out three Pokeballs, not six. There are only five Pokeballs on his jacket, two of which he already used.
Corrected entry: If Team Rocket have been after Pikachu all this time, why would they say "Who's that pokemon" when Pikachu's silhouette pops up?
Correction: A reference to what they always say in the TV version.
Corrected entry: In the scene where Fergus first sends out his Gyarados(where he's crossing the ocean to New Island on it), it's lips are blue very briefly. I guess the water was pretty cold.
Corrected entry: When one trainer sets off to the castle, he is riding Pidgeot. In a later shot he is now riding a Fearow.
Correction: This has been submitted and corrected already.
The Fearow trainer is a different person completely. She has blond hair and is scene in a prior scene but never again afterwards.
Corrected entry: When Ash is fighting the pirate trainer near the beginning of the film, and the pirate guy throws out the rest of his Pokémon, Ash sends his Pikachu, who uses Thunderbolt to knock them all out. The thing is, one of the Pokémon sent out was a Golem - a rock/ground type. Electric attacks have no effect on ground type Pokémon, so, even if Pikachu's Thunderbolt was that powerful (which is ridiculously unrealistic if you've played the video game), the Golem should have still been standing.
Correction: The TV show and movies don't follow the same type advantages and disadvantages as the video game series. If an attack has no effect at all in the games, it has some effect in the anime. So Rock types can be affected by Electric type attacks. In the episode "Showdown in Pewter City" Ash's Pikachu got supercharged in the Pewter City hydroelectic plant and it never lost all that energy. So Pikachu's attacks DO effect the Rock type Pokemon. Pikachu's attack against Golem is a way of showing how strong and unique Ash's Pikachu is.
Corrected entry: When the Charizard Ash owns is burning Mewtwo at New Island, since when could Ash tell it what to do? In later episodes of the TV show, Charizard just sleeps when Ash calls him out. Did Charizard forget he was trained or something?
Correction: This has been submitted and corrected already.