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)
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)
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.