A pre-9/11 National Intelligence Estimate was entitled "Islamic Extremists Learn to Fly", and was apparently about Islamic people taking classes at U.S. flight schools.
The National Security Agency and the FBI were both independently listening in on the phone calls between the supposed mastermind of the attacks and the lead hijacker. Indeed, the FBI built its own antenna in Madagascar specifically to listen in on the mastermind's phone calls. The day before 9/11, the mastermind told the lead hijacker "tomorrow is zero hour" and gave final approval for the attacks. The NSA intercepted the message that day and the FBI was likely also monitoring the mastermind's phone calls. (The NSA claims that it did not translate the intercept until September 12th; however, the above-mentioned FBI translator said that she was frequently ordered to falsify dates of translations regarding 9/11)
Indeed, the military had actually drilled for aerial attacks with planes:
The North American Aerospace Defense Command (NORAD), the military air defense agency responsible for protecting the U.S. mainland, had run drills for several years of planes being used as weapons against the World Trade Center and other U.S. high-profile buildings, and "numerous types of civilian and military aircraft were used as mock hijacked aircraft". In other words, drills using REAL AIRCRAFT simulating terrorist attacks crashing jets into buildings, including the twin towers, were run.