I'm basically on the same situation. I concluded all locations, side missions, etc. 100% of the main game, nothing else to do(except DLCs)! But the freaking tropy doesn't pop up!!
Same here. I double checked the locations but the trophy Old Habits didn't pop up. I haven't also unlocked the trophy The End but I completed every missions. My game completion locked at 99%. It could be because I was playing on a boosted save?
I have the same problem too. I have all the locations and I have finished the game, but the trophies Old Habits and The End have not popped up. It looks like it is a common glitch. It is really unfortunate since those were the last trophies I needed to get the platinum. I really hope they fix it...