I have come onto a bug in which if you do not exit and reenter the game, and you start a new one, you won't get missing achivements.
For instance, I just strolled through the game like I would be playing without trying to look for achivements, got ending A, and then after the credits and the PSA immeditately started a new game pursuing ending B and all the missable achivements. And though I did everyting right this time, none of the achivements popped up. Started a new game again, did the same thing again - no avail. Then I quit the game, reentered it, started a new game again, and this time were able to get some of the achievemts I missed.