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.
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.
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.
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.