Factual error: The cut of steak they show has nowhere near the fat marbling of Kobe beef. It's just the cheapest cut they could find. (00:02:30)
Continuity mistake: When Hal is swerving into and away from the bee, during the close-ups, there is a white van behind Hal's car. In the wide shot, there is no van. (00:20:04)
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: 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)
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.
Revealing mistake: When Kristen starts taking her helmet off you can see her hair is actually a wig.
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.
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: When we see Dewey's friend at the table eating cereal he is eating cereal and the bowl is full of milk. In the next shot the bowl is full of cereal and there is barely any milk.
Continuity mistake: Hal speaks about having held Malcolm the moment he was born. But in the Season 2 episode "Flashback" not only was he not there for his birth, he didn't hold him immediately, instead he talked to Lois.
Continuity mistake: During the scene when Lois says that Malcolm is a genius, his arms keep changing position between shots.
Visible crew/equipment: You can see the crew right after the intro. (00:01:00)
Continuity mistake: Halfway through the episode, the bedroom door is open in the wide shot. In the over-the-shoulder and closeup shots, the door is closed. (00:10:09)
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)
Pearl Harbor - S6-E4
Continuity mistake: Reese had a lot of food in his bowl (when complaining about the low-fat food she has made them eat), then Lois puts food in his suddenly empty bowl. (00:05:25)
Audio problem: You can hear the new boss speak, but her mouth doesn't move. (00:16:30)
Plot hole: There is no way that Malcolm would have been able to write that message on his stomach. He gets found by the nurse and then we see him in a room getting some medicine and then he is in the operating room.
Suggested correction: Actually before is given some type of sedation before the surgery he is wearing a different hospital gown. He would have had enough time to write the message on his stomach when he was asked to change into the blue gown.
Helmut was afraid Malcolm would run off again, so he likely changed him into the blue hospital gown after he tied him up to the bed. Malcolm could not scribble the message if his entire body was restrained. In the operating room we see he cannot move due to the injection Helmet gave him which eliminates the possibility of him writing the note here. Malcolm probably convinced the doctor who ran the blood test to have one of the surgeons secretly write the note after they prepped him in the OR.
Audio problem: When Craig reveals Lois is innocent, his lip movements do not match the audio as he says: "Lois was right all along." (00:21:00)