Revealing mistakes: During the "Save the Citizen" scene, when Lash is blown into the air, you can see the line behind him that lifts him. (DVD Version)
Audio/visual unsynchronized: Warren's lips don't move in the over-the-shoulder shot of him talking to Layla in the Paper Lantern.
Continuity: At the Homecoming Dance, Mr. Boy offers Layla a drink. Lash reaches out and spills the drink on Mr. Boy's shirt, but there is still a good amount of liquid left in the cup. At the very next shot, however, when Layla is handing him a napkin, Mr. Boy's cup is completely empty.
Revealing mistakes: The Commander raises his arms, clenches his fists and grimaces in pain before the beam from the Pacifier hits him.
Crew or equipment visible: When Principal Powers disappears through the gym door, the stage light is visible beneath and behind Coach Boomer
Continuity: After Medulla says "Let's boogie!" and the group starts to dance, Freeze Girl can be seen dancing in the middle of the group. In the next shot, Freeze Girl is standing next to Warren.
Continuity: When Will is sent to the nurse, the nurse was wearing a stethoscope around her neck, but when she turned sideways to put the equipment back, she turned to face Will again, and the stethoscope was gone.
Revealing mistakes: Will doesn't actually step on Medulla's foot in the mad science laboratory.
Continuity: When Will Stronghold and the Commander in the kitchen, the dad slams on the counter and the knives stay perfectly straight. In the next shot they are tilted for no reason.
Incorrectly regarded as goofs: When The Commander & Will go down to the Secret Sanctum, Will uses his mother's pole which is on the left. In the next shot, Will is shown coming down the right pole. The next shot was taken from the other side of the characters, from the Secret Sanctum. Therefore, they are still on the same poles, just the scene looks different.
Audio/visual unsynchronized: When Warren first walks up to Layla in the paper lantern, the water pitcher he's holding is hanging down on his side. But in the next shot he's holding it up in front of his chest.
Continuity: During the battle between Royal Pain and Will, Royal Pain is thrown into the disco ball, which shatters. In subsequent shots, the disco ball is still intact, as well as casting light around the room.
Continuity: During the kitchen scene when Will tells his Dad that he has no powers, the sink faucet spout is initially facing left and in subsequent scenes the faucet spout is facing towards the right.