Corrected entry: At the end of the first film, Mewtwo had wiped everyone's memory of him, but in Mewtwo's Return, Ash calls him by name as he carries him to the spring, even though he shouldn't remember it. Ash claims Meowth told him, but Meowth didn't know what his name was, and no one else told Ash his name, so how does Ash suddenly know Mewtwo's name?
Corrected entry: Whenever the clone Meowth talks, if you listen hard enough it's possible to tell that it isn't saying its name or variants on it. Instead, it says 'nyaa' and 'nyaarth' - the Japanese name for Meowth. Apparently they decided that it sounded enough like it was supposed to to make it not worth getting a voice-actor for the Meowth clone. Interestingly enough, I believe the Meowth clone in Mewtwo Strikes Back /did/ say its American dub name.
Correction: Actually, EVERY wild Meowth has kept its Japanese voice, including the TV series and the first movie. 4Kids probably figured that the wild Meowth's "Nya" was close enough to "Meow" or that the sound was closer to sounding like a real animal (such as Gyarados). The only Meowth that have been dubbed over are Team Rocket's Meowth (before it learns to talk) and the Meowth in Boots that appears in the Hoenn League Championship (apparently so that the dubbers could add in references and jokes to Brokeback Mountain).
Corrected entry: During the early days of the TV series, there were many rumors going around that Giovanni, the head of Team Rocket, was Ash's father. This was the first (and so far, only) time the two meet, yet they don't seem to recognize each other. This film disproved that rumor.
Correction: Ash's Father left when Ash was only a kid, around the age 2. Ash is at least 11 in this movie. Nine years have passed, so they wouldn't recognize each other.
Corrected entry: When all the good guys are in jail, they try to figure a way out, and then happily escape when the explosion from the factory destroys the jail cell. Now, we see that the bars aren't electrified, as Ash grabs onto the bars many times. Why don't the cloned Pokémon just break out of there? I'm sure that giant Gyarados could easily break those metal bars.
Correction: The Pokemon only do what their master or trainer tells them to do. In the case of the clone Pokemon, Mewtwo is their trainer, so they won't do anything unless they are specifically told by Mewtwo what to do.
Corrected entry: In the scene where Mewtwo is caught in the beam from the two robots, Ash, Brock and their pokemon destroy the red robot, and the black robot goes haywire, then it switches to the shot with Mewtwo falling, then back to the shot with the black robot, which miraculously, is now red.
Correction: Both robots turn a bright red when they start torturing Mewtwo.
Correction: Meowth was there when Giovanni called Mewtwo by name.