Continuity mistake: When Kim and Shego stop chasing Ron back in Drakken's lab Shego is wearing a purple apron, then the camera moves away Shego and Kim then comes back and Shego is not wearing a purple apron, then the camera moves away again and then comes back to her and now she is wearing the apron.
Other mistake: In the scene where Drakken accidentally "clones" Bonnie Rockwaller instead of Kim Possible, he holds up a picture of Kim to compare the results of his experiment with the real thing. The Bonnie clone, completely encapsulated behind the glass of Drakken's cloning machine (as evidenced by the reflection of light off of it) somehow manages to get a hold of the picture despite this barrier. (She does this without having to break the glass.).
Other mistake: After Ron pulls the monkey hair for Wade to analyze, Wade says something about placing it on the scanner. Then a tray comes horizontally out of the top of the Kimmunicator. The tray is about two and a half inches long, and the Kimmunicator is about half an inch thick. The tray is too big to fit in the Kimmunicator's top.