Continuity mistake: In the first movie the "Welcome to Silent Hill" sign is on the right. In this movie it's on the left.
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).
Suggested correction: The air is poisonous to them because they believe it to be. Your fears are manifested there. That's why everyone's Silent Hill is different.
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.
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: When Heather is in the elevator, and the monster slashes it up, the hole on top changes to a bigger cut in the next shots.
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 Rose is in the mirror, her hand is under the husbands, when she removes it his hand moves along with it, but his real hand doesn't move.
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.
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: When Pyramid Head cuts the prisoners arms off, one falls in front of Heather, the distance between heather and the arm change between shots.
Revealing mistake: When the blind guy puts the Seal or key into his chest you can see for the first two times he "hits" it to his chest, that he is not hitting himself at all.
Continuity mistake: When Heather comes home to see that her dad is missing. She sees the Come to Silent Hill, and the lamp is some what on the chair's arm. When the cops come in the room the lamp changes.
Continuity mistake: When Heather is in the mall and sees the guy hanging upside down, the way the man rips the flesh looks and moves is fake, you can see the hole of were the flesh ends.
Revealing mistake: During the final fight, when the Missionary is "sawing" through Pyramid Head's metal helmet, if you look closely, the helmet has been pre-scored and that the actress playing the Missionary is just running the blade along the pre-cut line in a "sawing" motion. The "metal" of the helmet also blatantly bends like rubber during the moment, revealing it's not really metal.
Revealing mistake: When Heather is in Silent hill, (right after the Mannequin part.) and talks to Alessa's mother, if you look at her nostrils you can see two rings of clean skin. (the rings are there for make-up reasons) but then after the flashback they are gone.
Revealing mistake: Throughout the final fight between Pyramid Head and the Missionary, you can tell that Pyramid Head's mask and sword are very light-weight and made of rubber or another soft-material. Ex. When Pyramid Head hits Missionary out of the arena with the hilt of his sword, in the wideshot, if you look through the flames, you can actually see the sword bobbing about in the air before the tip hits the ground as the actor can't keep it steady.
Visible crew/equipment: When the cart falls over with the nurses, when it hits the ground, the camera shakes.