Plot hole: In this episode Dewey tells Francis that their aunt died from a cat eating her face (or something involving a cat mutilating her face) and we find out this is how she really did die. But then why would it be an open-casket if her face was destroyed?
Suggested correction: Morticians can do fantastic work - this is very common.
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.
Plot hole: Hal says that his father was never there when he got dumped. But in episode 7, "Francis Escapes" Hal tells Francis he's never been dumped.
Kicked Out - S4-E12
Plot hole: Malcolm mentions how his parents would flip if they knew he was still dating his lying girlfriend. But in the episode before (while in the car with Lois, at the end) he mentions how his girlfriend has him guessing what she wants to do. The way he says it, makes it known that he is still dating her. He says it in present tense. Therefore, they already know for sure, from his own mouth.