I've learned when all the repairs are made, sometimes they stop. If your flak guns or deck gun is damaged, make sure your guns are manned and put them at station so it will be repaired.
The damage team only works in shifts so every four hours, you have to recall them. If they don't stop, you have to refit to get them to hush. I really detest this part of the game. I would like to strangle them when they start that.