Same here. I got Red Prince achievement even though he was not with me.
I played Beast as my main and completed the entire quest line including making nice with Justinia and agreeing to work together before she wanders off for good. However, the quest in my journal still says I need to confront her even though I already did and it did not close. So I never got any achievement for Beast even though I did finish the quest line and he was my main character.
I was on great terms with both Ifan and Fane and I think I did every thing needed for their quest but didn't get any achievement for them.
Also, Ifan was alive and well at the end of the game and we had a nice "best bro" conversation about what he plans to do next but my journal says he turned against me and was killed. Totally not what happened but maybe that's why I didn't get an achievement for him?