It seems we got off easy on our journey. We could have encountered something like Flight From London Detained at Dulles, More Than 200 Passengers Questioned Over Five Hours by Federal Officials (note that “officials said that several international flights have been similarly screened, including at least one other airliner at Dulles”), or the Osama 'fin' Laden problem.
Update: More evidence that we were lucky our flight landed without being stopped by someone: Two Flights to U.S. Canceled in Wake of Terror Concerns.