A *%#&@$#! men. At the very least a way to blow safety or pump fore and aft trim tanks or blow selected ballast tanks or something. In real life even traveling all day and night on the surface they made a daily trim dive to get the boat balanced fore and aft, and as close to neutral buoyancy as they could. The actual sequence was flooding negative and bow buoyancy tanks on the surface (the safety was always flooded, they called it the safety because if the ballast tanks were holed blowing the safety would give positive buoyancy) after the low pressure blowers emptied the saddle tanks (main ballast), and when doing the trim they calculated the amount the negative needed to have for near neutral buoyancy. On diving they would open the vents for the main ballast tankS (plural, many, not just one!) starting with the forward tanks so the bow would go down first, then open the others in sequence fore to aft. Passing 40 feet the command is given "blow negative to the mark", whatever mark they decided on when they did the last trim dive. In case of flooding in compartments they could "put a bubble" in any of the main ballast tanks (those are NORMALLY either empty or full but you CAN blow air into different ones for more buoyancy, since the air is compressed the inner and outer pressure will match and the tank won't collapse) or pump from / blow compressed air into any of the internal tanks to compensate. They completely ignore the most important aspects of operating a submersible vessel, buoyancy and balance management, in every sub simulator I've ever played.
As for the CO2 buildup, like everything else I found that out the hard way. Once I discovered it I changed the numbers to various different values (which are way off if they're in meters, unless they're Martian meters or something, 25 feet should be 7.6 meters, not 8.5) and ran a bunch of tests to determine what the actual depths are - 21 feet or above will get the crew on deck, 22 feet you can operate the deck gun but the crew won't man it, 23 feet will pop you back inside if you're on the deck gun. You can man the AA guns at 38 feet but not 39, even though you're underwater at 38 feet. At 35 feet you can still be on the bridge but underwater. 29 feet no battery discharge, diesels running, 30 feet diesels quit and the battery starts going down. Dive and stay under for a day or so, see the CO2 level at about 50%. Then come up and rise gradually, the red instantly vanishes and you get the message "oxygen level 100%" at 21 feet, same depth that the crew comes up. The instant effect is realistic, but in actuality the conning tower hatch is opened as soon as it clears and the main induction is opened at about 25 to 27 feet, as soon as the deck is about level with the water. The boat is then ventilated through the main induction, so if needed you can pop up, ventilate the boat, and dive again with a complete air change in a minute or so. The 21 foot depth part is the only thing that's really wrong, if the diesels are running at 29 feet where do they think the air is coming from?