Update: The bug has been fixed.
The Blueprint bug and rank glitch in C2W for #MGSVTPP are now fixed with the latest patch 1.04.
— KONAMI Europe (@konamieu) October 6, 2015
Some players are encountering a bug in MGSV: The Phantom Pain that prevents them from obtaining an S-Rank in a certain mission (and thus prevents them from unlocking the achievements / trophies that are tied to getting an S-Rank in all the missions and completing the game).
The problem occurs when people play the Mission 4 (C2W) after destroying the comms equipment in free roam. Since the objective of the mission has already been met with the comms equipment destroyed, it will result in a blank rating (-) on the mission list. Once you get this rating, it will stay there, even if you replay the mission and get an S-Rank. Furthermore, if you already had an S-Rank in this mission and you replay it with a – rating, the problem will occur as well. The blank rating will remain on the mission screen and be counted as such. All in all, this bug means you won’t be able to unlock certain achievements or trophies that require getting the S-rank for every mission.
On Steam there is a provisional solution to the problem, which you can find on the reddit post. Konami said they are looking into the issue. In the meantime, make sure you do not select Mission 4 after having destroyed the comms equipment.