I had exactly the same problem with the Safety trophy, I tried everything from doing it in Dark Matter Mode, deleting my savegame, and so on. At last I found a solution:
- Backup/Delete your savegame.
- Delete the entire Game from your Playstation.
- Download the game from PSN again (I first downloaded the activation key and then the game itself).
- Start the game, go to options -> unlock features and unlock the last levels.
- Play the level 24 ("200") again without loosing any tree -> Throphy poped up
Hope this helps people having trouble with some trophies in Eufloria. People tell that the Pacifism and Hero trophies cause troubles, too. Maybe this approach applies for this sort of trophy problems.
@Dyson-Team: Thanks for the great game! If you ever plan to create a new release, make a "very hard mode" for me and some more trophies, please