Other mistake: When Twoie first appears he is naked because he was just made. Yet when he walks toward the mirror, you can see at the bottom a strip of blue jeans.
Visible crew/equipment: When the mouse escapes from the cage at the lab you can see the handler's hand trying to lure the mouse.
Visible crew/equipment: When the lab rat gets out of the cage in the beginning of the movie, you can see a hand stopping the rat from falling off the table.