It's been told many times that this can happen in very heavy seas, when the ship is only hurt by your torpedoes, but the very reason of her sinking can be the huge waves and so on. It's also been told, that:
- a ship can go down without any hit just because of the storm,
- a ship can go down because of Luftwaffe/Kriegsmarine attack, collision, friendly fire (yes!

), and possibly some other reasons.
Maybe that's it?