Audio problem: Near the end when the family have got back in the car Malcolm says something like "who would have thought a traffic jam could be so cool, we should do this again". Near the end of the sentence we can see Malcolm's mouth and it isn't moving.
Dinner Out - S2-E4
Continuity mistake: When Lois and Kitty Kenarban (Stevie's mom) are at the table in the restaurant, while Hal and Abe sit at the bar, things on the table change position or disappear and reappear between shots. Same thing happens at Malcolm's table with Reese and Stevie.
Reese Cooks - S2-E18
Audio problem: When the girl Krelboyne is talking loudly, you can see her mouth barely matches anything she's saying.
Visible crew/equipment: Towards the end, right after they watch the house blow up, you can see a hand holding a black object popping up from the right side of the screen. This happens right before Malcolm says, "Pretty sure".
Continuity mistake: When Francis gets pulled over, his window is open and closed between shots.
Reese Cooks - S2-E18
Continuity mistake: During one of Reese's cooking classes, Hal puts some bread into a toaster. It then cuts to a shot of Reese. When it cuts back to Hal, the toast that pops out of the toaster isn't the same shape as the bread he put in.
Halloween Approximately - S2-E2
Other mistake: In the scene where boys are loading eggs into their slingshots, one of the eggs misses and falls on the roof, but doesn't break. A real egg would have broken.
Visible crew/equipment: When Lois gets in the car after she gets offended by the fact that everyone in the family forgot her birthday, you can see a cameraman with the camera reflected on the rear window when she leaves. (00:10:15)
Visible crew/equipment: When Reese throws the sheet off the bed a hand can be seen in the bottom right corner. (00:12:40)
Other mistake: At the beginning of the episode when they are driving in the car, the door is opened to make room for the camera outside but the opening is visible in shot. (01:49:00)
Reese Cooks - S2-E18
Visible crew/equipment: When Eric comes in to check on Francis, some crew members can be seen on the far left side of the screen. (00:13:45)
Factual error: It would be impossible for Malcolm to fall on the pins because the pinsetter is above them.
Dinner Out - S2-E4
Visible crew/equipment: Towards the end when Stevie punches Reese for the first time, his wheelchair swings back and a crew member holds and steadies it.
Continuity mistake: Craig mentions that he must have mailed the numbers from Lucky Aide to his mother, but later in the show (the episode with his fit dad), he doesn't remember his mother.
Continuity mistake: Francis asks for a doctor, and the cadets throw beads on his neck in response; the beads are missing in the next shot. (00:10:38)
Other mistake: The book Reese is sawing through in the background, while Malcom is talking into the camera, is already cut in half and the saw is not sawing anything. Then they cut to Reese about 7 seconds later as he actually saws the book in half. (00:02:13)
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.