Why did my crew suffocate while on the surface?

[Platapus]

Playing 1.5+ RFB

Just completed a photorecon mission and was sneaking out of the harbour. Was discovered by destroyers and received minor damage. Eventually I was able to avoid the destroyers and maneuver out to open water.

I was at Silent Running and the crew was not at battle stations. As per the manual for RFB I had the deck crew safely stowed.

Then it starts getting strange.

I secured from silent running
Surfaced
Called the crew to battle stations and verified that the DC crew was activated.

Strange occurrence 1. The minor damage to my sub would not get repaired after running for over two hours.

I secured from battle stations but kept the DC crew active.

Decided to head to port.

Strange occurrence 2. I noticed that the CO2 levels kept increasing even though the sub was on the surface.
When I went on to to the bridge I noticed that I was the only one there.

I cycled the deck crew from "hogans" to their stations and no change. The crew was not exhausted and only one watch was sleeping and one watch was "on duty".

My whole crew suffocated while the sub was on the surface.

Has anyone else run in to this bug?

The only thing I can think of is that while approaching the photo recce target, I had to pause the game for quite a few hours due to RL issues.

Any idea what happened?