This is the second time this happened to me.
Out at the Docks in Sanhok the speedboat that's sometimes between the two large boats is sunk. The first time, I heard the motor running and depended on it being there when I was ready to leave. I swam around for a minute, but couldn't see any boat.
The second time I heard the motor and jumped in the water to look for it, thinking it was behind something. There it was, as you see, miraculously running under the water. I even tried to drive it, thinking maybe a speed boost might help it resurface, but nothing.
The video and bug report have been submitted.