Sign out of your PSN Account and then sign in again. Now, in the game's menu, go to EXTRAS and select PERSONAL STATISTICS. Scroll down to find a checklist related to your missing trophy there. Make sure that every trophy-related quest is listed as "complete". If not, create a new save slot and complete the missing trophy activities. In order not to start from the beginning of the main story-line, choose the "Start from Quest" option after pressing the Advanced key.
Try doing the above in the New Game Plus mode, if the method fails at first.
If all of the aforementioned steps fail, try the following: