When Hobo Jojo picks up the newspaper and begins to read it, the Dear Donna section on the back page has the line "Dear Donna, I am faced with the difficult prospect of completing an entire animated feature in less than six months," and then continues on. This may be a reference to the real film's shortened production deadline. See more...
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Continuity: 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: 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: 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: 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.