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 required in-air refueling shortly after attaining low cruising altitude. It always took off with low fuel, because it was safer, and extended the lifespan of the tyres and brakes. (Not because it leaked fuel, although that's also the case, but the amount actually lost on the ground was relatively negligible). Without refuelling DARYL would have run out of fuel long before his flight ended.
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.