Visible crew/equipment: When Hal rebuilds the track of dominoes, he walks out and slams the the door. This starts the dominoes falling. When it comes up to a shot of the American flag in dominoes, if you look closely to the left of the screen you can see a hand pushing it over.
Other mistake: In this episode Malcolm's new teacher begins a league table for the Krelboyne class, and since Malcolm shows that he is better than the whole class, the teacher creates a new highest rank for him which he calls "1 to the 11". However mathmatically, "1 to the 11" is still 1, so it seems rather strange that the teacher would go the trouble, and that none of the class would notice this.
Hal Coaches - S3-E16
Continuity mistake: After Malcolm pushes the computer off his desk, you can see it still on the desk in the next shot, when he says "this means nothing." (00:17:17)
Health Scare - S3-E6
Continuity mistake: When Lavernia gets knocked out by Francis during their fight, her head is turned to her left. A shot later, her head is turned to her right.
Continuity mistake: When Lois fights with the woman in the mud puddle, the tug of war rope is seen dropped on the ground, and then tense again. This alternates between close and far shots.
Factual error: It's very very unlikely that police would chase all those women through town (even take helicopters to arrest them) just for making noise on someone's property for couple of minutes.
Answer: Francis is only allowed to talk on the phone at school for three minutes a day. I think the code gives him free access to talk to his girlfriend.