Factual error: When the F-16s take off to shoot down the Blue Thunder, both planes have the same tail number 068. All military jets have individual tail numbers. (01:30:25)
Factual error: Cochrane chases Murphy in a Hughes 500 which has a top speed of 147 mph and easily keeps up with him, demonstrating that Blue Thunder's top speed is less than 150 mph. The F-16s sent after Blue Thunder have a stall speed of 175 mph. They would have to slow down to the point of falling out of the sky to have a shot at Murphy. Its utterly impractical and far more likely that the military would have sent AH-1 Cobra attack helicopters after him.
Suggested correction: Not necessarily. The F16 (and other fast movers) can and do engage slow moving helos all the time. They just engage them by missile from a long distance, where speeds are irrelevant.
I'm no expert, but I wouldn't think the US Military keeps helicopter crews on Alert Status like they do for fighters. This film was during the Cold War, so maybe, but it wouldn't make sense to keep an attack helicopter crew (and ground crew) on Alert like they would for fighter jets. Even after 9/11, I wouldn't think a (armed) helicopter crew would be beneficial to keep.