Character mistake: In the scene where Steve and Josie prepare to leave to fight the giant robot at the beginning of the movie, Steve tells Will "Oh, Will, a reminder: a lot of the kids at Sky High will only have one super hero parent, not two." When he says "one super hero parent", he holds up two fingers. When he says "not two", he holds up only one finger.
Revealing mistake: There are multiple times throughout the movie when the "wind effect", the hair of the characters being blown up by wind off of Speed's super speed, is not in sync and occurs prior to Speed actually zooming past. The 2 most notable occurrences of this are when Speed steals the pudding from Ethan and moves next to Lash and when Speed steals the Pacifier from the secret sanctum.
Continuity mistake: In P.E., after Warren says, "Hey! Get your head in the game!", while Coach Boomer is giving them the rules to the game, the timer switches on, and the citizen gets lowered down. When the citizen starts out, its feet are pointing toward the timer board, but in the next shot, its body is parallel to it.
Continuity mistake: When Layla is being attacked by Penny she fights back using the plants, and breaks the window. As Penny is informing Layla that Royal Pain had broke the anti-gravity device the window is still broke, then the camera goes back to Penny and then again to Layla and to the right of Layla's head you can see the window fully intact again.
Continuity mistake: When Will and Layla board the school bus near the beginning of the movie, Ron the driver chastises Will for asking if they are on the right bus and slams the door behind them. A few minutes later, when the Ron announces they are off for Sky Camp, he is shown pulling the "door close" handle again.