Deliberate mistake: In the final shot of the film, Jill's head moves slightly when she's supposed to be dead. In the commentary, Wes Craven confirmed this wasn't strictly intentional, but he decided to leave the take in on purpose in case he decided to bring her back in a future installment. But unless a sequel proves she's still alive, it's technically a mistake, albeit a deliberate one.
Factual error: Winter in Antarctica would not have a night and day as portrayed, with the amount of light changing so much during the course of 24 hours.
Plot hole: No one wonders what happened to all the staff and patients at that sanatorium? No police ever came there and checked the place out after 30 years? And all the patient records, furniture, etc are still there?
Factual error: When Nate dies by the alien moon rocks, his helmet visor "explodes." The visor in the film shatters like glass, but the real visors on actual spacesuits are made of polycarbonate, a plastic that does not shatter but deforms.
Plot hole: Everybody jumps into the water and emerges on the submarine except for Natalie. They're wondering where she is when they notice a flare. They realise it's her, and they send a search party. She's hiding on a bus maybe one to two kilometres away from the water. Her going there makes no plausible sense. Makes no sense how she held her breath underwater longer than anybody that they didn't see her and why she would go in the opposite direction of the sub. It was done to prolong the scene. (01:09:00 - 01:18:00)
Continuity mistake: During the bridge collapse scene, when Olivia is crawling on the beam, she is first seen on the part of the beam that is closer to Sam. Almost instantly afterwards, she is on the part of the them that is closer to Molly. The space between the two beams increases significantly between the two shots as well.
Factual error: The Song "Looking for the Magic" by the Dwight Twilley Band plays on repeat several times throughout the movie, however it comes up as track 1 on the CD player each time."Looking for the Magic" was never the first track on a Dwight Twilley CD - It was track 2 on the group's 'Twilley Don't Mind' album released in 1977. You can tell the disc is not a homemade mix CD by the printing on the top of the CD the first time it is placed in the tray.
Revealing mistake: While driving the Mercedes to the house of grandma, the gauges on the dashboard show speed is zero and the engine is cold.
Continuity mistake: When Valerie's father was the werewolf, his right paw was burnt. Then, when we see the hand later, there isn't a scratch on it, but again later, we see that it is, once again, looking burnt.
Visible crew/equipment: When Jack arrives with the shopping, a crew member in shorts is reflected on the glass. Clearly not Max.
Continuity mistake: When Justin gets a text from Mike's cell phone, it shows a close up of the screen. In the "to" box, it says Nikki although it's Mike's phone.
Continuity mistake: When Charley and Ed are arguing in the abandoned house, the light switches on the wall next to Ed change positions repeatedly between shots even though neither of the characters ever touch them.
Continuity mistake: When Lucy comes home at the beginning of the movie she quickly buttons the top of her dress. While eating dinner, it is open and then buttoned again between shots.
Plot hole: The very last scene shows Mary building a wall, apparently in her belfry. But there should still be the original wall that Rose built, with the hole in it that Mary smashed in. By killing Rose / having killed Rose, she prevents further harm, but all effects that took place before that (also the building of the wall), should stay (like her scars). It is very unlikely Mary broke down the whole wall just to add another body. (01:28:25)
Factual error: The young priest sees images of a red-eyed horse, but later, it is referred to as a mule, which looks much more like a donkey.
Factual error: Mallory tells Florence that the school is in Cumbria. Cumbria didn't exist in 1921. It was created in 1974 from Cumberland, Westmorland and part of Lancashire.
Continuity mistake: In the scene where Lily is hiding behind Thomas' computer desk, she uses her little Eiffel tower necklace to put inside the socket to short out the power. When she goes to put it in, you can see the computer is plugged in on the bottom socket. After a really quick cut scene, the computer is now plugged in on the top socket. (01:05:00)
Continuity mistake: After Sarah finds her father in the bedroom and goes downstairs to get help, the blood pattern on her shirt/upper breasts changes. While the movie is edited to look like one continuous shot, it was filmed in bits and pieces, and the blood pattern was not consistent in some of the shots, it seems.
Factual error: Colonel Meyer's promotions are listed in his SS ID card as Hauptmann, Oberstleutnant and Oberst. Since the SS used a different ranking system from the Wehrmacht, they should actually be Hauptsturmführer, Obersturmbannführer and Standartenführer.
Revealing mistake: As the guy is being pinned down by the giant hooks you can see for over a minute he can simply escape and slip his hands out. (00:52:30 - 00:53:30)