Trophies not unlocking

So I've just finished my first playthrough and a couple trophies that I should have unlocked, just aren't.  One of those trophies should be because it's a story related one and the 2 other that I'm sure I should also have are tied to the faction ranks.

I'm honestly just a bit confused and mildly frustrated that they didn't unlock. I do plan on playing through the game again, it's just a little annoying that I kind of have to just to get these.

If there was a way to get them without having to play again just to get them, I would really appreciate it.

Trophies missing: Part 10: The Blood of Arlathan, Annihilation in Arlathan and Call for Coin and Company.