Factual error: While the problem with refuelling the SR71 is a real one for D.A.R.Y.L., he is never going to get that far. The SR71 had no self starters and required a trained crew with a starter generator mounted on a truck to get the engines going in the first place. D.A.R.Y.L. just pushes a button and away he goes. Not likely.
Factual error: DARYL steals an SR-71 Blackbird reconnaissance plane toward the end of the film. Conceding the absurd notion that a kid could fly it (computer brain or not), the problem is that SR-71 requires an in-the-air refueling shortly after attaining low cruising altitude. This is because the fuel tanks are designed to leak on the ground - the friction of high speed flight expands and seals them - and the afterburners required to get the plane up guzzle fuel. DARYL would have run out of fuel long before his flight ended, and the Air Force did not send up a tanker for him.
Factual error: When you see D.A.R.Y.L. in the SR-71 Blackbird there are many shots of the cockpit. There are too many screens, in fact, the only "computer" screen in the Blackbird is in the copilot's part of the plane, D.A.R.Y.L. also did not have a copilot. If you don't believe me, check out http://www.wvi.com/~sr71webmaster/image2~2.html.
Factual error: At the time the SR-71 was operational, it was classified as black ops. That is as highly classified as you can get without actually knowing what it is about. The security details for the SR-71 were armed guards stationed around the plane 24/7. Anyone getting near the plane would be shot without questions. The idea that only a trip wire and a single guard dog were watching over this highly regarded secret plane is absurd.