Plot hole: So he needed the help of a big strong burly guy to flip the safe with the body, end over end to the pit, but he somehow was able to easily get it out of his basement and into the back of his car by himself?
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: Throughout the first half of the movie the focus is to locate and find David Park. It is believed this will lead them to Bragga and they can arrest him. However, later in the movie it is revealed that Letty was working with the FBI and was killed running drugs for Bragga. This means that the whole storyline to find Park was useless because they already knew how to get people inside. (00:18:55)
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: The UN agent boards a 50-year old Russian cargo plane, has to ask the pilot, Delphy, where the hatch is, and yet immediately accesses the triggering mechanism, down to knowing which of the connectors is for the explosive bolts. How likely is that?
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: There is a scene when Terrence tricks Big Fate into touching his "lucky pipe". Terrence then plants it at the murder scene in order to rightfully implicate Big Fate in the murders. Terrence then goes to the police station and tells Beniot about his strange feeling that the perpetrator smoked crack while committing the murders, and suggests Beniot comb the scene again. Terrence's fingerprints were all over the pipe as well. He couldn't wipe his fingerprints off without wiping Big Fate's off as well. Since it is a requirement that all police officers have their prints on file and since Terrence isn't the officer to locate the "evidence", how can he explain his fingerprints being all over the pipe? After all that has happened, I would think he would have implicated himself.
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: Miles arranged the chase with the streetcar, so that Danny would have to take out the transformer and shut down the power in the area, in a way that it would remain shut down. How could he know that the dumb operator would leave the FBI guy on hold for as long as (s)he did? Someone said after the streetcar finally stopped, "they turned off the power."
Plot hole: While breaking into the vault, Gabe and Ripley use a reciprocating saw to cut a block from the concrete wall. The block is several feet thick, quite beyond the reach of a saw of the sort. The view after the block is cut also shows no holes where they would have had to drill to get the cut started. (00:56:00)