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: There is a scene where Heather pulls the mask off one of the cult-members, and the air literally poisons him, causing his skin to discolor and his throat to choke up. This never happens before or after. Vincent claims that those particular cult-members have superstitions about the air being poisonous, but there are a multitude of problems with this explanation: A) We have seen numerous other people go unaffected by the air, and B) we later see several of these same cult-members in the sanctuary, unmasked, breathing the same "poisonous" air with no adverse effects. (And Claudia had stated that even the sanctuary is no longer safe from the darkness of Silent Hill, so they are technically breathing the same "poison" air that's outside).