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. (00:17:50)
Continuity mistake: When the "Krelborne" teacher comes to the house to tell Lois that Malcolm is gifted, Lois comes to the door naked and puts her arm up on the doorway. On the shot from behind she has her hand low (about where her waist is) from the shot from the front she has her hand up high (above her head).
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.