[KaleunMarco]

Originally Posted by NeonsStyle

I did encounter an odd error. The game day before, I was
attacked by aircraft and they damaged the 20mm AA gun which could not be moved to the repair window.

The next day, I was shadowing a lone ship setting up an attack. I'd ordered the boat to track west. After awhile, I noticed we hadn't made the turn. Then I noticed the engines were off. So I set Standard and the crew responed with "Unable to Comply". So I tried the electric engines, same thing. No response and unable to comply. So I checked the ship damage, but there was only the 20 mm AA gun which had now moved to be repaired. It had full fuel, full battery so it should've worked.

I couldn't move the boat at all! She was dead in the water.

most likely you left your crew at Battle Stations for too long and they fatigued. all of them. the only way to cure this is either to restore a game from a previous time, or wait (and pray) for your crew to recover and then proceed.

Originally Posted by NeonsStyle

Another problem is CO2, even on the surface, it's 100% and I can't get it down. Is there some trick to get it down? You'd imagine on the surface
it'd just be pumped fresh air in and co2 out.

i'll bet you like to alt-tab out to Windows and do something else. best advice is to not do that when playing SH4.
the fix is to save and exit the game. then, relaunch SH4 and reload the game-situation. the CO2 level will return to zero.