Ok guys,
I've finally nailed down the bug related to "kapitan, torpedo doors are closed" :
The offending units are :
The bug is activated only when you go in the F1 station.
So if you choose Alfa, play the mission without never going in F1 station there will be no bug. Its only when you go to the sub control station that the message starts and is repeated again and again. And when you exit all russian units will have the problem.