Considering it had sunk twice before, I fail to see why its sinking is "a mystery."
Its sinking is a mystery because it completed its mission and then apparently displayed the blue light to the shore indicating the mission succeeded. Then it sank. Nobody knows if it was due to some kind of enemy action, a defect in the sub, or a fatal error by the crew.
Anything in the water can submerge. Surfacing is always the hard part.