Two unknown people show up at a secret government facility in the middle of the night.

I think it seems quite reasonable that the security of the site (which may have been entirely robotic) would detain and separate the intruders, until they can ascertain what threat they are and what to do with them. Separating them seems reasonable from the point of view that talking to them individually may reveal more and people are less of a threat when they can't cooperate as a team.

It's not clear exactly what time of the night this happens, but it's not early. Its after dark and it is summer time (they are growing crops).

Its entirely possible that the senior staff were off-duty at the time. It may have taken some minutes to ascertain that Cooper was who he said he was, and decide that it was worth introducing him to the senior NASA team.

Two unknown people show up at a secret government facility in the middle of the night.

I think it seems quite reasonable that the security of the site (which may have been entirely robotic) would detain and separate the intruders, until they can ascertain what threat they are and what to do with them. Separating them seems reasonable from the point of view that talking to them individually may reveal more and people are less of a threat when they can't cooperate as a team.

It's not clear exactly what time of the night this happens, but it's not early. Its after dark and it is summer time (they are growing crops).

It's entirely possible that the senior staff were off-duty at the time. It may have taken some minutes to ascertain that Cooper was who he said he was, and decide that it was worth introducing him to the senior NASA team.