Plot hole: When Rane and the other terrorists come out the bottom of the plane and start walking towards the fairgrounds, it is amazing how not one police officer or staff member of the airport notices that they came out from under the plane, or that they don't seem to be walking off the plane like the other passengers.
Plot hole: When the police and FBI arrest Rane at the fairgrounds, Cutter tells them Vincent (one of Rane's men) is also at the fair, and wearing a tan jacket. Cutter did not see Vincent leave the plane and never saw him at the fair, and when he last saw him on the plane he was not wearing this jacket. So how could he know Vincent was at the fair and wearing a tan jacket?
Plot hole: The airport at which the plane lands is only supposed to have a small airfield. Yet near the end we see the huge plane roaring down the runway for more than a minute, which would be impossible on a small airfield.
Plot hole: Liz Hurley, who is one of the hijackers, learns that Cutter is an undercover security agent. Yet for some reason she fails to pass this on to any of the other hijackers. When they take over none of them appear to have any knowledge of Cutter.
Plot hole: While Cutter is in the bathroom, the first thing he hears of the terrorists taking over the plane, is one of them yelling "sit down". If he heard that, how could he have not heard the gun shots when Ms. Ritchie shot the FBI agents, or the sounds of screaming passengers?
Answer: It's been a while since I've watched this movie, but he obviously knows the plane is hijacked. It's a pretty safe assumption that the agents are dead as they're escorting a dangerous, high profile prisoner. Pretty easy to connect the dots. Alternatively, they could've failed to check in, and he assumed the worst.