Character mistake: As Team Rocket discovers the cloning machine made by Mewtwo, they start naming the shadows of each Pokemon as they appear on the screen. As the first Pokemon appears on screen, they say "Alakazam" but it is actually an outline of "Scyther" who is a different type of Pokemon.
Character mistake: When Chessy confronts "Annie" when she's presenting her with the big breakfast, she's talking about when Annie was on the phone the night before. Then she says her father overslept, when she actually meant to say and "and you overslept," as the conversation doesn't make any sense saying that the father overslept. (00:58:00)
Character mistake: At the beginning of the movie, Marnie states that she is 13 years old. When Grandma Aggie comes to visit, she tells Mom that it is Marnie's 13th Halloween. Since everyone celebrates their first Halloween before they turn one, if Marnie is 13 the events of this movie would occur on her 14th Halloween, meaning her powers would have faded by now.
Suggested correction: As explained in the DVD commentary, Team Rocket don't know everything about Pokemon. They thought it was an Alakazam though.