When Corin Nemec is drinking coffee on the ramp and looking at the iris, the pattern of debris on the ramp is entirely different when shown from the control room than when shown from the gate room. Even which of the fluorescent lights on the ramp railings have been damaged has changed.
O'Neill is wearing a MBU-12 O2 mask while piloting the X-302. The mask is missing the preamp which means it has no microphone. The mask is also missing its pigtail (wiring harness) which also means he has no audio going to his helmet. He could not be communicating with anyone as shown.
After Jack O'Neill ejects from the X-302, Walter Harriman says,
"Patching in satellite imagery." However, the image which displays on the monitor is clearly shot from a helicopter.
Area 51 is shown to have grass along its runways.
However, it's located in the Southern Nevada desert alongside of a dry lake bed. There is no grass along the runway as there's not enough water to maintain it.