Continuity mistake: When the boys are wrapping their parents present, Dewey is holding a bow in some shots and not holding one in other shots.
Long Drive - S4-E11
Visible crew/equipment: When Lois is yelling at the boys there is a camera visible on the left side of the frame. (00:01:40)
Continuity mistake: This mistake happens in the scene where Dewey bumps his head. In one shot, Lois puts her hand on Dewey's shoulder, and in the next shot, her hand is on his chest.
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)
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.
Continuity mistake: While Dewey stands on the table, Mrs. White (Bea Arthur) dips her finger in the bowl of chocolate and draws a mustache with it on Dewey. In the following shots the chocolate on Dewey's face differs.
Visible crew/equipment: Towards the end, right after they watch the house blow up, you can see a hand holding a black object popping up from the right side of the screen. This happens right before Malcolm says, "Pretty sure".
Other mistake: When it is Dewey's birthday Malcom grabs a piece of the cake. It goes to Dewey then back to Malcom and he is chewing, but there is no bite in the cake.
Continuity mistake: In the escape scene when Hal runs out the store his boss presses a button to lower the shutters. This causes the pencils to fall out of the cup but in the next shot the pencils are back in the cup and roll off the table into the fan.
Continuity mistake: When Francis gets pulled over, his window is open and closed between shots.
Continuity mistake: In the scene where Lois and the boys are in the clothing store, Lois piles a bunch of clothes in Reese's arms. The clothes change in his arms from shot to shot.
Reese Cooks - S2-E18
Continuity mistake: During one of Reese's cooking classes, Hal puts some bread into a toaster. It then cuts to a shot of Reese. When it cuts back to Hal, the toast that pops out of the toaster isn't the same shape as the bread he put in.
Continuity mistake: When Julie passes through the kitchen to get Malcolm, Dewey and Egg are in there cleaning the floor they have suds all over the floor, When Julie runs back through after seeing Malcolm in his underwear she slides across the floor, The floor is still completely covered in suds but when she gets up if you look in the background you see the floor with hardly any suds anywhere. She could not have soaked up all the suds when she slid across.
Continuity mistake: When Lois is in the bath tub soaking after getting upset about the family wanting to go to the funeral. Dewey comes in and ask for juice. When they are on Lois(front view) the suds barely come to the top of her breast. When the show Dewey (side view of Lois) The suds are all the way up to her shoulder.
Other mistake: Lois wins the truck, which is never seen again.
Suggested correction: Just because we're not told what happened to the truck doesn't mean a mistake occurred. There's a number of valid reason we don't see it again (especially when only 3 more episodes were produced in the series).
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.