Factual error: At the inauguration party, the band sounds three "Ruffles and Flourishes" and then "Hail to the Chief" for the departure of the President. The President should receive four "Ruffles and Flourishes" prior to "Hail to the Chief", and both are sounded only at his entrance, not his departure.
Factual error: 26,000 people work in the Pentagon. If they were to all file past one person so he can try to pick out a crime suspect, and each person takes just two seconds to walk past, be checked, eliminated and sent on their way, it will take fourteen and a half hours to clear the building. There are going to be some very unhappy people at the back of the queue.
Factual error: The Pentagon is the largest office building in the world. It has seven floors, 28 kilometers of corridors and 620,000 square metres of office floor space. The idea that the entire building could be searched in one afternoon by six people is beyond absurd. If those six people could search an average of one office every five minutes and they worked twenty four hours a day, seven days a week they'd get through the whole building in 89 days and 15 hours. I don't think the punter they are looking for has a lot to worry about.
Continuity mistake: During the room-by-room search in the Pentagon, Kevin Costner deliberately spills coffee on his uniform to avoid the witnesses seeing him. There is a huge wet spot on his left rear and down the back of his pant leg. A few seconds later, after he has excused himself to go to his office to change his uniform, he is seen in the hallway, only now the coffee stain is visibly smaller and more on the front of the pant leg.