When Professor Keenbean activates RoboBee to help in shutting the molecular re-organizer machine off, the long-shot / closeup of RoboBee getting ready to attack Ferguson show's Keenbean's mouth not moving when he yells "Fly like you've never flown before!".
When Van Dough is getting the temple message, he gets mad at his secretary for going counter-clockwise. When he grabs her hands and does it for her, he is going counter-clockwise, too.
The fax appears in the fax machine after it has been removed.
Richie looks in the mirror at a pimple next to his nose, but later when he asks his dad if he can see it, Richie points to his chin.
When Van Dough ties Keenbean up, he puts the sandwich on his chest. In one scene, the bread of the sandwich is brown. Then next it is white. Then it was brown when Richie got out of the machine, and then it was white again.
When Richard opens the plane window to throw the TNT out of the plane, there is so little wind that even his hair doesn't move.
Near the end of the movie, Richie fires Mr. Van Dough. When Mrs. Rich punches him in the face, you can see Mr. Rich's arm move from pushing Van Dough away from them as if the punch was really strong.