The missions "Hit the Gas" and "Valley Armed Convoy" disappears if you advance too far in the story as i've noticed.
Im sitting on 50/52 missions completed and it annoys the crap out of me.
I have also 15/14 Cult Properties Destroyed. This might be cus of one of the silos "wasn't there" or invisible and when i destroyed it, there was just an explosion sound that cut of and nothing more. I later returned to that silo and viola, it was there. This might not be the case but that's my suspicion