This has been dealt with several times before. Also when you have a CO2 warning a little pop-up warning appears in the upper left corner (where you'll never look for it). Clicking on the CO2 warning pop-up button is supposed to surface the sub and open the hatches. Surfacing and just expecting the crew to open hatches doesn't work as they are not smart enough to do that before they die...
Try the button to see if it works. It always does for me and others. A few have had to save, exit and reload. I don't have a clue why. Call it a feature, not a bug!:rotfl: