Revealing mistake: In the scene where Rocky and Bullwinkle are walking through the university with Kenan and Kel (right before they come across the anti-moose protest), Kel's right arm passes through Rocky's left several times.
Continuity mistake: In the scene when the FBI agent is in the TV tower early on in the film, you see her put the FBI Identification card thing back into her 'mobile phone holder' in her bag. Then you see the guards charging up the stairs. Then the shot goes back to the FBI agent. She hasn't put her ID card thing inside her bag yet, she is still holding it.
Character mistake: When Boris and Natasha (Jason Alexander and Renee Russo) are at the airport (just missing Rocky, Bullwinkle and the FBI agent) Natasha says something about "Moose and Squirrel don't even know our names", yet earlier in the courthouse scene, Bullwinkle says something about Boris and Natasha being real people and Rocky and Bullwinkle still being cartoons.
Other mistake: When Rocky jumps off the lighthouse in a failed effort to fly, he falls and hits the ground. Once on the ground, we see his goggles are unevenly on because of the crash. However, one of his goggles actually goes through his head.
Continuity mistake: When Cappy von Trumpet says "it's almost as if there's a mole in the white house", it shows a mole. Then, after Cappy says "yes, sir" we see a view of the president's desk and the mole isn't anywhere to be seen. Then, when Agent Sympathy says "ROCKY AND BULLWINKLE!" in a very excited voice, we see the mole surprised.