Plot hole: The killer has been living in the (apparently big enough) crawlspace between walls and floors, for over a decade. There is no explanation (or rationale) given on how he moved the various objects inside every room, closed doors, fed when the house was not occupied, hid the various corpses and, silly detail, concealed his own BO and the stench of his own living quarters, which is something hinted at when they find out his hideout. It is explicitly said that he is agoraphobic and does not get out, ever.
Continuity mistake: After Mike has set the tent up they go for a ride on their snowmobile to check the scenery out. They come uphill parking the snowmobile facing upwards. They get up looking at the scenery, and a few shots later the snowmobile has suddenly turned 180 degrees facing downhill. (00:13:40)
Other mistake: Aladdin slices off one head of the monster in the tomb. The body spurts copious amounts of blood and the severed head even bounces on him repeatedly, but Aladdin's shirt is immaculate afterwards. (00:04:40)
Continuity mistake: When Sheriff Cooper writes "Karsson" and underlines it on the chalkboard, the way it is written changes between shots. In one particular shot, the line he underlined it with is suddenly rubbed out.
Factual error: When the underground garage of the market is flooded, the car that Kyle and Heather are in does not flood. A car is not water tight like a submarine. Even though the water does not cover the top of the car, water would flood the entire car within minutes.
Continuity mistake: In the underground lab, Dr. Su offers to surgically remove the false memories he implanted in John's brain. He drills a half-inch hole in the right side of John's forehead, which leaves the right side of his face covered in flowing blood. John can't stand the pain, breaks free, and he goes on a rampage throughout the underground bunker, killing every UniSol in his path. As he fights his way through the bunker, the bleeding hole in John's head switches from the right side of his forehead to the left side, then back to the right side again. Also, in the last scene (an unspecified amount of time after the bunker brawl), John has no scar on his forehead at all.
Other mistake: After the daughter visited with her mother for the first time, she is reviewing the footage with the priests. No such camera angles were taken for what they reviewed, only an overhead room camera would have been available.
Revealing mistake: When Three Finger is driving the truck to ram the car containing Angela's husband you can see round the eyes that it is a mask being worn.
Character mistake: When Michael goes to the antique shop, the sign out front is spelled wrong; it reads "anitques."