The goof item below may give away important plot points.
When Drakken successfully activates the Tempus Simia in Africa, he opens a time-space portal behind him to escape. Shego, Monkey Fist, and Drakken escape through it; it disappears just as Kim lunges at it. But the fourth criminal at the scene - Duff Killigan - never made it through. Yet in the next scene with the criminals, Killigan is with the whole group as if he hadn't been left behind.