Same here. Sunk a troop transport with a hit to the stern. I was about to put in a second torpedo (or maybe a third) to finish it off, but to my surprise it suddenly sank, some 20 minutes after I first hit it. The first time I've seen a ship sink to flooding.
It too hit the bottom once, then carried on drifting through the sea bed. Once it disappeared, the sounds all stopped too. Maybe it's designed that way to help performance... ? Either way I don't like it. In shallow waters you no longer have obstacles to avoid. Remembering where you sank the ships on 100% realism is all part of the challenge