Another person reported this CO2 thing. I have not seen it yet.
I HAVE, however, seen compressed air spontaneously run out after ordering a crash dive. It only seems to happen when crash diving, normal dives don't affect it. However it charges back up when you surface.
With that though, I have noticed a positive feature: it seems like compressed air is actually used by the boat while manuevering now instead of being a basically useless stat.
And weird. Today I reloaded the save game from yesterday where my crew wasn't leaving the conning tower, and they now go in properly again when I dive. Go figure!