Continuity mistake: While Dewey stands on the table, Mrs. White (Bea Arthur) dips her finger in the bowl of chocolate and draws a mustache with it on Dewey. In the following shots the chocolate on Dewey's face differs.
Continuity mistake: When Malcolm and Reese talk about April at the water park, there's a girl with a blue shirt and a towel tied around the pelvis who passes behind Malcolm twice in two different shots.
Halloween Approximately - S2-E2
Continuity mistake: When Francis walks into the boy's room the calendar says September 2000. In the next shot it changes to October 2000. After that Reece says "No, it really is the 31st" he flips up the September page of the calendar to October. (00:06:15 - 00:07:15)
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.
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)
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.
Continuity mistake: In the bowling alley, the design above the pins is blue and pink pins. While in the back of the bowling alley, above the pins is a different design.
Continuity mistake: In the side of the story when Lois takes the boys, Malcolm has some kiddy bumpers put in to help him bowl. In the next scene when Reese is about to tell Beth the joke, you can see the lane which Malcolm was just at but there are no bumpers in the gutters. Then later when Malcolm stands up to Lois they are back in the gutters.
Continuity mistake: When Francis gets pulled over, his window is open and closed between shots.
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.
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)
Continuity mistake: When the Tarantula is put on Hal at the zoo, the shot is only of a yellow shirt with the tarantula crawling on it. When the shot changes to where they show the whole Hal, you can easily tell that the tarantula is fake - it is larger than it was and is in a different spot on Hal's shirt.
Humilithon - S4-E2
Continuity mistake: When Hal starts to fight with Lionel with the mop at the school when Hal turns his back you can see it is wet from the mop a few scenes before he hit them and then the frame before Lionel strikes Hal with the mop his shirt is dry again. (00:17:05)
Continuity mistake: In the scene where Lois and the boys are in the clothing store, Lois piles a bunch of clothes in Reese's arms. The clothes change in his arms from shot to shot.
Kicked Out - S4-E12
Continuity mistake: Malcolm's seat belt changes from on to off the first scene with him and his mom in the car. When it's a shot from the front it's on, but when it's a shot from the side (from the driver's/mom side) you can see that the part of the seat belt that's going across is now behind Malcolm, instead of on him like it was a second ago. This changes back and forth.
Continuity mistake: In the escape scene when Hal runs out the store his boss presses a button to lower the shutters. This causes the pencils to fall out of the cup but in the next shot the pencils are back in the cup and roll off the table into the fan.
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.