This is a bug from the most recent patch that I've seen others talk about. I want to report that I'm experiencing it too.
I'm on a new character doing the Pentagon Missions on Story Mode for the first time.
Here is what happened:
- Playing solo, I traveled to the Pentagon for the first time.
- I completed the Pentagon Breach mission and unlocked the giant door that leads to the next Pentagon mission.
- The next Pentagon mission can't start. It says I'm missing the requirements, which are: Complete the Pentagon Breach mission.
- Because I completed the Pentagon Breach Mission, I don't have access to it anymore.
To summarize, I completed the Pentagon Breach mission (and now it is gone from my map), but the game didn't register it as complete, so I can't access the other Pentagon missions. The Pentagon Breach mission is now gone from my map now so I can't replay to get another complete.