In the episode when Francis runs away from military school, he and his father are talking in the van. There is a pair of headlights behind them following very close, but when seen from outside, the car is driving down the rain soaked road with no car behind them.
In the episode when Francis babysits, they clean the house. They realize it is now *too* clean and start blowing dirt out of a vacuum. As the camera backs up, the ceiling disappears, revealing the top of the set.
At the end of Lois vs. Evil, Malcolm speaks to camera with several children moving in the background. One boy doesn't know where or when to move and he tries to speak to someone off camera. In the end he gives up, shrugs his shoulders and walks off.