Plot hole: After the scene at the Houses of Parliament where Irene Adler escapes through the sewer from the clutches of Lord Blackwood, she suddenly appears at Tower Bridge, about 3 miles away. Even assuming she ran there and the journey was skipped, going there makes zero sense. It slows her down, leaves her exposed and limits her exit points - she's got all of London to escape into! (01:48:00)
Plot hole: Towards the end, Patrick takes the 5kt bomb into a helicopter and climbs it away to safety. The problem with that is that the helicopters have a rather low rate of climb - ~10 m/s for military helicopters, less than that for civilian ones. This is the rate of climb at low altitudes, and it is with altitude. He had less than 5 minutes to climb, which would put the bomb at most 3000 meters above the city, and more realistically, one tenth that - just about the optimum height for the bomb to inflict major damage on the Vatican city and the center of Rome.
Plot hole: When Abby and her kids are abducted, the sheriff is sitting right outside her house and sees this happening. Yet the video didn't record. Well the sheriff saw it all with his own eyes so why wouldn't his testimony hold up? The tape actually shows the UFO so there's proof right there. (01:08:55)
Plot hole: At the beginning there is an audio recording of Thomas talking to the police. He explicitly says 'They killed her! They Killed my sister, my mom!' or something to that effect and that Thomas was arrested for the rape and murder of his sister and he killed himself in custody. At the end, his sister is killed and the little epilogue says that the sister's body was found in her brother's arms and when their mother found out about the 'death of her children' she killed herself. That doesn't make sense logically. Thomas was alive when his mother was dead, according to the clip at the beginning.
Plot hole: When the girl looks at the photos of Martin and his father while on the business trip, Martin is seen with his father and while wearing his boarding school sweater. But Harriet says later that he wasn't sent to boarding school until after their father was killed. Therefore, the sweater would not have been a clue in the earlier part of the movie.
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: 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)