Factual error: The whole basis of the trial and conviction of Cameron Poe is a crock. The judge can not arbitrarily mete out a sentence that is harsher based on the ability of someone to defend him/herself. In justifying the harsher sentence because of Poe's military skills, the judge effectively says that Poe is more guilty than an average person due to his honorable and decorated service in uniform to his country. In my entire time in law school, I never read one out of the literally hundreds of cases I was assigned in which a judge issued a harsher sentence because of someone's innate or learned abilities to defend themselves. But since this was a movie court room proceeding, the fact that Poe had a witness to the fight (his wife), the fact that he was injured in the fight, and the fact that his uniform was torn and otherwise ruined as a result of the fight are never examined. A D.A. wouldn't have taken this to a grand jury on a bet, because they would have never returned an indictment or "true bill."
Factual error: After the hijacked plane departs Carson City, they are pressed for time. We can assume they fly a direct route to Lerner Airfield, not flying any doglegs. So flying over Fresno can not have been a deviation, it must be on a direct route from Carson City. Lerner Airfield, however, is exremely dry, wide-spread desert land, but such type of land doesn't exist in the lush areas of California South of Fresno, on a straight line extended from Carson City beyond Fresno.
Factual error: The tour plane departs Carson City, but shortly later Larkin says that the hijacked plane was over Arizona (still believing it to be the hijacked C-123, not knowing yet that the tour plane has the transponder of the C-123 on board). Even if we take the NorthWestern-most area of Arizona, that would be over 300 statute miles from Carson City. That small plane can not fly over 300 miles in that short time.
Factual error: The tour plane flies way too fast and way too close to the buttes on its scenic tour. For one thing, that prop plane type cannot fly that fast, and secondly, no tour pilot would ever fly that fast and close to the surrounding terrain. Such a tour would most definitely be operating according to Part 135 of the Federal Aviation Regulations, but even if operating under Part 91 (which a commerial tour cannot be) it would violate the FARs in terms of minimum safe altitudes, minimum lateral distance from obstacles/terrain, and the catch-all "reckless and careless" clause would apply as well. (Notice this happens already before they're confronted with the Cobras.)
Factual error: When John Cusack is driving the old Corvette to Lerner Field he shifts the car. He is going way too fast to be shifting from second to third so apparently he is shifting from fourth to overdrive. The only problem is that five speed transmissions weren't available until much later. In fact, on these old transmissions, shifting up and to the right from fourth would put you in reverse.