If you're experiencing issues continuing progress on a trophy, there are a few things you can try in order of complexity:
- Restart the game
- Pin/unpin the trophy
- Create a manual save based on your existing file (OPTIONS > MANUAL SAVE) then restart the game. Choose your file, select LOAD GAME, and then choose the manual save. Attempt the trophy requirement(s) straight through without loading checkpoints or dying.
In most extreme cases, you may need to start a new save file with the intent of completing the respective trophy requirement, as they should trigger with a refreshed playthrough.