I think, but I'm not sure,you may have encountered the save game bug which relates to saving close to ships that are rendered.you have to save at least 50Km away from any ship or sinking that you have caused,otherwise they will respawn and you will get no credit for the sinking,also it makes a mess of game saves if you save to close to sunken/unsunk ships,limitations of the game I'm afraid

something to remember next time if this is the fault