Trivia: At the fairground, when Rane and the two terrorists walk away as Cutter is arriving, there's a white Honda Civic seen. It's license plate reads "outatime", the same as the plate on the DeLorean in Back to the Future.
Trivia: FBI Agent Dwight Henderson is portrayed by Robert Hooks, the father of director Kevin Hooks.
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.