This has likely been an issue during all my playthroughs, but as this is my "final" playthrough (i.e. my own personal canonical one, so to speak) I've gone to great lengths for everything to be "perfect"; this includes finishing all objectives on every mission.
Unfortunately, cue final mission ("Infiltrate Alpha Protocol"), two objectives refuse to update when finished - "Save Mina" and "Escape Greybox".
When I finish Save Mine, it says that the objective is finished, but when I check my map/Intel, it's not. She appears on the boat at the end (I wonder where Sis & Scarlet went; especially Sis) and everything checks out, but when the mission screen is brought up, it says 8/10 objectives finished.
I know some triggers have been wonky, especially in the Checkpoint department (whomever thought that a checkpoint system was a great idea should be kneecap't), so I've tried "walking around" the points in which these things should logically "check out". But no dice.
Been through the mission three times now, but those two objectives refuse to finish.