When retrieving the sunken lockbox with the notes in it, if you just read the notes and don't take them you can't progress in the quest... even though the quest removes the marker for the lockbox and instructs you to discuss the notes at a new location.
I had to spend an hour swimming around the bay trying to locate where the lockbox was. Luckily I came across it. If I had put the game down for a week and this happened, I would have had no recollection where the lockbox was.