Plot hole: The police Inspector recounts the murders, comparing them to the ten Biblical plagues of Egypt, and he states that in keeping with this theme Dr. Kitaj was killed by rats. First, Dr Kitaj dies in a plane crash. Okay, he was attacked by rats in flight but nobody would know that - his plane crashes in a huge, violent fireball and nobody would find any rat remains after that. Second, there was no plague of rats in ancient Egypt! (Go ahead, look it up). Even if the police had made the connection between the mysterious deaths and the ancient plagues they would not make the connection here.
Plot hole: When Harry is on the roof of the first shooting, he finds the spent shell casing. Later in the office he says that they think it is a 30-06. He has the shell casing. He *knows* if it is a 30-06 or not.
Plot hole: The sergeant tells Stone that he only has to listen for a bell for an important communication coming through and will then alert the rest of Wildfire. Yet later, Dutton notices a message already printed out. So at a facility this important, the sergeant just ignores the machine if it prints out a message and doesn't ring? He has to have clearance to read them or they wouldn't print out where he is. It's a bit too convenient for the plot that he wouldn't visually check each message to make sure.