Other mistake: Lois wins the truck, which is never seen again.
Suggested correction: Just because we're not told what happened to the truck doesn't mean a mistake occurred. There's a number of valid reason we don't see it again (especially when only 3 more episodes were produced in the series).
Continuity mistake: When the boys are wrapping their parents present, Dewey is holding a bow in some shots and not holding one in other 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.
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)
Kitty's Back - S6-E5
Visible crew/equipment: A hand is visible on the left edge of the screen when Francis is talking to Dewey through the bathroom door. (00:15:50)
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.