Bad luck I assume, although Ive never reached patrol #13. Usually Im either dead or retired by that point.
As to the sudden mysterious damage either you found a mine, an un noticed aircraft, or shore batteries spotted you. Although you did state you were in the middle of no where. Did you do any saves / reloads during this patrol? If you save a game with prior damage, every time you load that game the damage gets announced all over again
The Co2 thing is a known bug. A save and reload should fix it. By the way the air compressor has nothing to do with that. Its a ventilation system which is not really modelled.
Dont really know... good luck on your next... Maybe its time to consider retirement