Agent 99's hairstyle changes from when she's pretending to be a manicurist, to a later scene, when she's meeting with Chief.
When the Chief shows Max and 99 the picture of Jimmy Ballantine in his office, the close up shot shows Ballantine wearing his prison number. But in the wide shots there is no number.
When the Chief is showing 99 and Max the image of Ballantine, distant images have no ID number but the closeup has one.
In the opening, just before the credits, when the KAOS agents shoot up Max's car, the camera jumps and the tree shadows change after Max and 99 duck out of view. After the squibs damage the windscreen, the camera and shadows jump again, and the tree shadow on the wall is a completely different shape.