I only say this because if you go through all other missions OFF Site.
IE:
Kenly College
The Zoo
Camp Oak
Coney Island
Operation Dark Hours
You all go through either the Helipad or fast travel to mission start.
But the Pentagon you have an actual Safehouse like the main map and when you load in you get the same message as if you are in a safehouse in the LZ/Main map and there is a vendor and your stash box like all other safehouses., that seems a bit strange for a single mission when all offsite missions don't.
Maybe we'll never know but I definitely don't think the Pentagon area was supposed to be a single mission.
Ooops mistake in title was supposed to say (was and not were)