Continuity mistake: When Mojo Jojo's monkey clones start attacking Townsville, there is a giant barrel rolling towards a dog. When you first see the barrel, it's rolling at a reasonable speed and is only a short distance away from the dog when Buttercup sees the barrel. The shot goes to Buttercup, who is a good distance in the air. When Buttercup flies down to save the dog, the barrel is in almost the exact same place. Given the distance between the dog and the barrel in the first place, the dog would have been rolled over long ago.
Continuity mistake: In the scene towards the end of the movie when Mojo Jojo has the Powerpuff Girls in his hand while climbing the large building, the girls are in his right hand. While Mojo is still climbing the building, the girls are in his left hand. If Mojo had put the girls into his other hand, they would have been able to escape Mojo's grasp easily while he was switching hands.
Continuity mistake: When the girls go to school for the first time, there are a few shots with the clock and alphabet shown. The first shot shows the clock changing from 9-12 and the letters (part of the alphabet) above reading "Qq,Rr,Ss". In a later shot, the letters above the clock read "Kk,Ll,Mm,Nn". In the next shot when the professor and Ms. Keane walk out the door, the letter above the clock changes to "Gg".
Continuity mistake: When the chrome ball falls in the tag scene, there's a pointy top on the top of the ball, and the broken supporter on the bottom. But when the ball lands on the street, those things are gone.
Continuity mistake: As the chrome ball is traveling through the town, it is reflecting a stationary image of the town, not the actual part of the town being shown.
Continuity mistake: After the lady rudely grabs the baby rattle away from Bubbles, Blossom consoles her while Buttercup yells at the lady from behind them (according to the camera's point of view). When Mojo tells Bubbles not to listen to the lady, the girls are automatically standing a straight, horizontal line, with Blossom in the middle.
Continuity mistake: When the girls are flying all around the loft at the Utonium house after the tag scene, it's pretty obvious that the flying patterns are repeated two or three times, as the girls end and begin in two completely different locations.