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.).