Yeah... for example Kaidan.
I tried to like that guy, I really did, but he was one stubborn bastard. But god dammit, Kaidan, I did not save your *** in the 1st game only to be forced to shoot it in the 3rd game while trying to apprehend Udina.
And another example is Padok Wiks (he replaces Mordin if he dies in the 2nd game), a likable guy, no doubt. But he just wouldn't give up on his self righteous goal to cure the damn genophage. And, due to my poor dialog options, I couldn't peacefully prevent him from doing it.