Plot hole: Peter goes into Carl's mind to save Catherine. When he's in there he sees the tank with the water nymph. On the tank are strange symbols which provide the FBI with the clue needed to find the latest victim. Makes sense so far. But, go back to the scene just after the FBI have captured the comatose killer and are looking in his basement. The FBI are looking at the contraption that the killer uses to suspend himself over the victim. On the contraption is the same symbol seen later on the water nymph's tank. Why didn't the FBI follow up the symbol then?
Plot hole: When Alex and Clear are sitting and having coffee they are on a corner. He looks in the window to see the bus pass, and as he looks to see if it is there, it's not. As the camera pans across the street, there is some construction going on which is blocking that whole road from being used, but then Terry, Carter's girlfriend gets "waxed" by the bus - no way it could have got through all that construction.
Plot hole: When Kuzco and Yzma make a dive for the potion bottle, Yzma is turned into a cat simply by landing on the potion bottle. This suggests that a person only needs to touch the potion in order to be affected. However, when Kronk and Yzma are serving Kuzco dinner and are trying to avoid poisoning themselves, Kronk pours his potion drink on himself and is not affected.
Plot hole: When Wolf and Tony find Virginia in the Huntsman's tree house, she tells them that he chained her up, so she can't go downstairs and open the door from the inside. However, after Wolf climbs her hair and enters through the window, the two of them walk down the stairs without any chains stopping her. They couldn't have cut her free with the magic ax because Tony was holding it, and he was downstairs by the door.
Plot hole: After Jade sees Jaspers transform, she flees and calls the cop Margolies on his cell from a pay phone. It's pretty unlikely that in her panicked state of mind she'd remember his number by heart, especially since he only gave it to her that same day.