Visible crew/equipment: When Dewey yells for Lois because the bow was put on the present, if you look to the left of Lois, you will see a crewmember kneeling down, handing Lois the red dress, who is holding a bucket of water. He quickly gets out of the camera's view. [This is on the DVD of the first season. Someone said on the audio commentary that after catching it, they deliberately left it in to see if anyone would spot it. It's still a mistake, but that's why it's there.]
Continuity mistake: When Malcolm is trying to get the TV back to the channel he was watching, he picks up a big remote and finds the channel which the video camera feed is on, but the remote he is holding on the TV is a smaller one. It then cuts back to Malcolm who is moving his hand away from the remote he just put down and it's the bigger one again.
Continuity mistake: Episode 16 Season 6 "No Motorcycles." Francis calls Hal out to the driveway where two motorcycles are parked. In the first camera shot the motorcycles are parked side by side with the front wheels turned in the same direction. All subsequent shots of the motorcycles in the driveway show them in a different position, one angled behind the other, with the front wheels turned in opposite directions.
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 scene where Lois and Hal tell Malcolm he is going to the "special class", Hal notes that the pitcher of iced-tea he makes is always empty, and says, "Look at that - gone," before placing the lid back onto the pitcher. Yet, when it cuts to the wide shot of the table, the pitcher lid is by Hal's elbow.
Continuity mistake: In the episode "Bride of Ida", in the scene where the grandma is talking at the table with Reese and Malcolm, notice the bottle on the table next the the grandma, between takes the cork from the bottle goes from being on top of the bottle to next to the bottle, it changes in almost every different shot.
Continuity mistake: Episode 111 Season 6 "Pearl Harbor" Lois and Jessica enter the house after coming back from going to a musical. As Lois comes through the door her purse slips off her shoulder and she catches it around her elbow. In the next shot a second later, the purse is back up on her shoulder.