Factual error: The nuke is provided by the military, not NASA. There is no reason why the NASA guys should have any access to the bomb. So, the idea of some random technician at Mission Control punching in a few numbers on a keyboard and somehow shutting off the bomb makes absolutely no sense.
Other mistake: If the meteor shower that hits NYC is the same one that destroyed the shuttle, how was so much time able to pass that all the newspapers were able to report on the shuttle before NYC got hit?
Suggested correction: Good question. Nobody says that it's the "same" shower though. All of them come from the bigger rock, and they are coming in intervals. So it could very well be some time had passed between showers. Also, the meteorites that hit the shuttle were much smaller and probably burned up in the atmosphere before bigger ones followed.
Factual error: Both shuttles are approaching the Russian space station with their main engines on, without atmosphere that would not be needed.
Visible crew/equipment: There is a reflection of the cameraman & crane in fume in the outside shot while A.J. and Lev discuss controls of the Armadillo, before they reach the canyon.
Other mistake: Adding on to the idea of the shuttles flying too close together, at a couple points the ejected shuttles from one booster appear to fly directly into the flight path of the tailing shuttle. While is certainly possible the second shuttle could maneuver to avoid the collision, it further demonstrates the absurdities of launching the two craft in such close proximity.
Revealing mistake: When it shows the first shuttle docking with the Russian space station, you can see the word "Force" on the side of the shuttle. When the second shuttle docks, its a reverse of the same footage, because now you can see the word "Force" is backwards.