Plot hole: It seems unlikely any mental institution would let a patient out to visit home for any length of time as happens in the movie with the killer and his mother.
Suggested correction: Unlikely, but still possible. Almost every workplace has a situation in which a person is bending the rules.
Plot hole: The Thorwalds were supposed to be in the apartment for only six months according to the lease, their phone number wouldn't have been published in the phone book for such a short lease.
Plot hole: The movie establishes that the FBI has a list of suspects thanks to security camera footage from the area where the victims were found. "A red headed man, two African Americans above average height, a white haired man." Then, the zinger; "a man in his 30s with a tattoo of a rabbit or an animal on his right arm", which of course is our guy Josh Hartnett. We see the tattoo, and it's a little doodle of a sheep, about a couple square inches big, below his wrist. That doesn't really make sense; if they have security footage with that level of detail, one wonders how could the rest be so vague. The next entry mentions "a male with a scar on his jaw", which is even more absurd. Either the security cameras picked those details up along with the suspect's full appearance and mugshot, or they just can't know with such certainty (if the suspect was masked or concealed in any way, then they would know for sure it was the killer and wouldn't be chasing people with wildly different appearances).
Plot hole: In the first film, the shape of the ring was a little different and it was set in a ring. Also, it was given to Xania. In the second film, she was never even acknowledged as donating it to the museum.
Plot hole: If the vacuum is strong enough to suck up a hand grenade, why isn't it sucking up the ampules?
Plot hole: The movie at best is being dishonest with the ending of the chase scene; to keep Dr. King as a possible suspect, the gunshot happens so shortly after she went out of frame (with no cuts) that (since she is -NOT - the killer) there is no possible way that the gun could have ended in her hand. There's also no possible way for the culprit to escape, to find Hassan in the crowd and be there at the perfect moment, etc. (01:16:35)
Plot hole: Every ghost that we see in the house looks the way they did when they died, for example the girl from the film's intro is seen without skin on her face, which happened to her before she died. However, in the final scene when we see Simon's ghost joining them, he looks completely normal, when he should have had a throat slit wound and the carved markings on his skin. (01:31:20)
Plot hole: In the scene in the hotel, David sees the victim's head on the floor after the killer left. Later when David is in a hospital bed he is watching TV and the reporter claims that all the heads were in Judd's car. The killer would have had to have gone back into the hotel room to get the head of that victim after David saw it. She would have put it in her bag right away if she was saving them all. The bag was even left behind. (01:12:30 - 01:25:00)