When Pistachio does the back flip onto the platform where Jennifer is standing, he has his back to her, but when he lands, he is facing her.
When Mr. Peru is asking the waiter for things that he doesn't have, the shrunken head in his hand disappears between shots.
When Pistachio is looking for an assistant, Jennifer Esposito puts on her bag when it was already on.
At Bowman's party, the Items on the waiters plate, as he offers them to Pistachio disguised as Mr. Peru, constantly change.
When the grandfather asks where the nest is and Pistachio says the attic, he is sitting down really close to the wall. In the next shot, when he stands up, he isn't even close to any walls.
One of the precious items depicted in the film was the Apollo 11 lunar module, which landed the first humans on the moon. The bottom half of Apollo 11 (the Descent Module) is still sitting on the moon today - it was for descent only. The top half, the Ascent Module, was jettisoned into space before the astronauts descended back to earth. So it is impossible for the actual Apollo 11 to be stolen as depicted in the film.
While in disguise, Fabbrizio Disguisey is shown carrying off the Liberty Bell on his own with his own two hands. This is an impossible feat as the Liberty Bell weighs 2'080 pounds, just over one ton. To put that into perspective, the heaviest weight carried by a single person is 1'216 pounds, just over half the weight of the Liberty Bell.
When Pistachio, as the "Cherry Pie Man", is fighting the two henchmen, the cherries he spits are flying at the "henchies" from two visibly different angles.
When Pistachio does a back flip onto the platform where Jennifer is chained, in some shots, one can clearly see the wires connected to his belt.
Two main revealing mistakes with the Turtle Man include: in between shots the glasses he is wearing change from being regular glasses to magnified glasses, and vice versa. And at one point when Jennifer is trying to get information from the cigar roller, you can see the bald cap Pistachio is wearing as the Turtle Man starts to come loose behind his right ear.
When Pistachio gets out of the cherry pie, he is covered in cherries and cherry juice, yet when he runs away from the guards, he leaves no cherry juice footprints.
When Pistachio, as the "Cherry Pie Man", is fighting the TWO henchmen, the cherries he spits are flying at the 'henchies' from two visibly different angles. Watch for the crossfire.
When Pistachio has the flashback in the gym, the guy says, "Think you got muscles now, try this." When Pistachio says O.K, his mouth doesn't move at all.
When Pistachio, as Prince Lallijamba, plays a song to the snake, the way he plays the recorder does not match the song in the background.
When Pistachio and Jennifer go to the toy convention to find Bowman she says her name is Barbara, and Bowman invites her to his house. When Pistachio comes looking for her at the door (as the German Guy and the Snobby English Guy) he says he needs to talk to Jennifer Barker. Wouldn't he ask to see Barbara instead of Jennifer? Also Bowman knows her as Barbara and didn't say anything about him calling her Jennifer.