Other 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.
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.
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: The first time the bus takes off for Sky High, you see the name change from "School Bus" to "Sky High School Bus." In the next shot it says "School Bus" again.
Continuity mistake: The school bus changes back and forth between a long and short version within several scenes.
Continuity mistake: In P.E., when Will and Warren are up against Speed and Lash, the first time Will gets knocked over he gets thrown against a wall. When he lands on the floor, he is pretty close to the wall. In the next shot, after Zach says "Ouch", Will is much farther away from 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: Kelly Preston's hair changes back and forth between shots, during the scene when the parents discover the party in their house, and in consecutive shots throughout the movie.
Plot hole: In the scene where The Commander and Jetstream are called to fight the giant robot, Will's mom says "What if he forgets his lunch?" In every scene where he's eating lunch at school, Will has a school lunch.