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).
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.
Audio problem: When Heather is reading her dads note in the car to Silent Hill, the letter and the voice over do not match. (the second paragraph starts off by saying: "But you desire" and the last word right before "I love you" is "place" but through out the reading you do not hear those words.
Deliberate mistake: When Douglas' fingers are chopped off, they are hit from the right side by the blade, but they inexplicably fly directly forward (instead of to the left as they shoot), somersaulting smoothly through the air in a clean, uniform manner. Obviously done for the sake of the 3D effects in the film as they fly directly towards camera, but completely defying the laws of physics.
Revealing mistake: When we see a vision of Child-Alyssa walking down the street with a sort-of vortext behind her as the cult-members flee, watch closely and the entire shot is comical. All of the extras are barely moving at a jogging-speed despite supposedly running for their lives from her. Several are visible running towards her direction or even directly behind her despite supposedly fleeing from her. Several extras veer off to the side before exiting frame even though there are buildings on either side so there's nowhere to go. And several others still are visible running left-to-right or right-to-left from either side of the frame, again despite there being buildings on either side. Obviously all of the extras were filmed in front of a green-screen being told "just run around a bit" and then added to the scene. The shot makes no sense if you pay attention.
Continuity mistake: At the end, when Claudia transforms into the final creature after touching the seal/amulet, her human body begins to disintegrate. As she screams and the scene cuts from a medium shot to a closeup, all of her hair suddenly vanishes between shots.
Continuity mistake: In the first film, "Red Pyramid" is portrayed as absolutely massive. (Judging by the scene in which he rips a cultist's skin off, he is about 10-12' tall) Yet, as evidenced in the final fight sequence, he appears to be significantly smaller in this film. (7-8' tall).
Revealing mistake: When Beast-Leonard is killed by having the Seal ripped from his chest, when he disintegrates, the shot goes completely out of focus as he begins to "burn up." All the more puzzling because the effect is computer-generated and only the background is real footage. Perhaps the background shot went out of focus and they had to purposely blur the effect to match? Either way, extremely sloppy work.