I've been playing the game 100% in co op with one friend, we've done every mission together and collected every collectable we have found at the same time and yet some times one of us will receive a trophy while the other will not. I'm talking strictly quest related trophies, the ones we should both be getting at the same time
A few xamples:
We killed the twins but only my friend got the trophy, for me it still says 1 of 2 killed.
We have found all the pages of the guide book, I have the trophy, he doesn't (even though the in game menu says we have all the same guides)
We reached Henderson together, I got the trophy he didn't.
We defended the cinema, again, I got it, he didn't.
We've done every Dead Zone together, I have the trophy he doesn't.
Ya I was wondering if that might have been the problem. Turns out I was an idiot and didn't realize he hadn't synched his trophies so that's why it looked like he didn't have the story related ones. But it doesn't explain what happened with the others (Twins, King among Kings, Heart of Darkness)
We went back and re did some of the areas and managed to get the other missing trophies, just strange it didn't award them to both of us the first time around.