Other mistake: In this episode Malcolm's new teacher begins a league table for the Krelboyne class, and since Malcolm shows that he is better than the whole class, the teacher creates a new highest rank for him which he calls "1 to the 11". However mathmatically, "1 to the 11" is still 1, so it seems rather strange that the teacher would go the trouble, and that none of the class would notice this.
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.