Plot hole: The motivation of the cult in this film - a dark entity trying to birth their demonic god - is completely different from the cult of the original film, which was portrayed as fanatical Christian witch-burners. No satisfactory explanation is given in the film to explain this and in fact the film explicitly implies they are the same cult on several occasions. The explanation that the cult of the original film is some sort of offshoot or different sect of the cult from this film cannot explain this as it is pure fan speculation and conjecture (thus non-canonical) and in fact raises several more plot-holes.
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.Charles Austin Miller
Character mistake: When Michael goes to the antique shop, the sign out front is spelled wrong; it reads "anitques."
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.Sammo