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.
Plot hole: Natalie uses her cell phone to record the injured and bleeding Chris, but it never occurs to her to use the phone to call for help? And how is it possible that in 2012, she seems to be the only one with a cell phone? It is simply not possible that she could not get a signal - the Chernobyl Exclusion Zone is festooned with mobile telephone masts - precisely because of the inherent danger of being lost there.
Plot hole: Marty Mikalski discovers a micro-camera in the cabin and is immediately grabbed by the cursed zombie Judah Bruckner, who drags Marty through the window and plants a machete in Marty's back. In that shot, the machete is obviously buried in Marty's back, which should have broken ribs both back and front, severed spinal nerves, penetrated arteries (as well as the right lung), and protruded from his chest. Marty was dead on arrival in that one stroke. Yet Marty emerges at the end of the film as the hero, with no gushing blood from his back or chest or mouth, and no explanation of how he miraculously removed the machete from his back.
Plot hole: Selene has been kept in a cryogenic tank for 12 years. And for 12 years the scientists running experiments on her very conveniently kept her boots and skin tight suit in the lab. Not just that: they did not keep them in a locker or in a box, but scattered across different shelves of the glass cabinet where they also store test tubes and big bottles of chemicals. Directly in front of them, in fact. (00:10:00)
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.
Suggested correction: Uri said at the beginning of the film that he has never gotten a signal whilst in that area.
Then Uri is wrong, or he is lying for some bizarre reason. The Chernobyl Exclusion Zone is festooned with mobile antenna masts and if there was one place on earth where you could absolutely guarantee getting a signal, it is there.