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?
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.
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.