Xbox One. Not sure if anybody else is having this issue. But I completed the Mendoza - Closing Statement secret mission. This should be the 4 out of 4 story missions you need for the Xbox Trophy. I have completed this doing both methods. Poisoning Yates (To Loyalty Challenge, which I got) and meeting Yates and Diana after they walk up to his room. The game will say Story Mission Completed. But when I replay or start another fresh mission it still shows this as uncompleted and the Xbox Trophy never goes off. Kind of annoying me, because its one of the last Trophies I have for this game.
This has always been the case since Mumbai having secret mission stories. Completed or not, these secret ones won’t be shown as completed in a fresh playthough. However, if I recall correctly, you don’t need to complete the secret ones to earn the mission stories achievements/trophies.
Anyway, I’d suggest you post this under the bug report thread to let the developers know the issue. It will be even better with a screenshot of the mission stories page.
The same thing just happened to me on PS4. I completed Closing Statement, and when I started again later, it was showing incomplete. Obviously, this would lock me out of the trophy as well, just as you are locked out of the achievement.