The private contractors (spoilers)
Maybe I just was distracted or something, but there seemed to be an unexplored mystery or conspiracy. The commander leaves to go to the main base some miles away. While he's gone, a unit of private security contractors shows up and tells them they aren't to leave the base, and this order is confirmed when they check it.
Was it ever explained why the private contractors were there? Why they had orders to not leave the base?
Was the government aware of the alien base? The contractors representing some intelligence group trying to study or capture it? You could even go out further on a limb that they represented some rogue faction that had made a secret collaboration deal with them and were trying to prevent the military from discovering and revealing it. Or they were being forced to stay in the base to serve as test subjects for the mind control army.
It almost seems like the contractor scene was part of a larger element of the film that got cut or couldn't be filmed because of budget constraints but got left in for other reasons.