Quite up until recently I was unaware of a certain what looks like, a bug or glitch with PSN Trophy’s on PS3. I didn’t notice it before until I went to go play Dead Island and Sonic Generations that I noticed I was receiving the same Trophies I’ve already obtained in the game from regular play. So I hit up a search on Google to see what could be done about it. It turns out that it’s something to do with the Trophy
Sync between your PS3 and the PSN Server with your account on it. What I have seemed to of discovered is that if you’ve obtained alot of Trophies for a certain game while connected to PSN, then go back and play them while signed out for a while, and you obtain more trophies for a certain game, then reconnect back online, I would probably say that the time frame would be 3-5 weeks maybe more of offline mode while playing games that have Trophies, that was roughly how long I was at the time due to Internet connection issues and constantly being signed out all the time, then asking me to update the system firmware, blah blah blah… then where I just decided to leave it signed out.
I’m guessing the whole thing about this weird glitch is probably a fail-safe to prevent people from cheating, trying to obtain a certain trophy without actually achieving it properly, or something like that, but what I did dig up that it is some sort of glitch that can happen sometimes, the simple fix to it is to just “Sync with Trophy Server“. So from the PS3 XMB screen go to Trophy which is under Game, then press △ to open the Side Menu then Press X to sync with the server, this may take some time to sync, but once this is done, go back into the game(s) that had missing Trophies and it should all be there again.