Factual error: When Cruise and Wallis are in the underground tunnel beneath London they are walking along the tracks before a Tube train blasts through. The 3rd rail is missing, which carries the electricity for London Underground trains and would have electrocuted them both if it was there as it should be.
Plot hole: When the C-130 transport is falling from the sky, the Egyptian sarcophagus remains lashed to the plane's cargo deck. The crew exploring the wreckage says they are miles from the 'primary crash site' (so that nasty stuff can happen to them without witnesses). The sarcophagus would still be at the primary crash site, along with the remains of the fuselage and cargo deck. (00:32:50 - 00:36:00)rgbfoundry
Stupidity: When Henry is talking to Nick, he feels himself beginning to change into Edward Hyde, he goes to his desk to inject the serum to stop his transformation. If he had injected himself before continuing the conversation, his transformation into Hyde would not have occurred.