it is a well known bug with sh4 that has never been fixed. it also can cause your watch crew to stay on deck when submerged and its caused mainly by alt+tabbing out of game but sometimes on rare ocassions it just happens for unknown reasons.
there are 2 ways to fix it, submerge then surface by clicking on the co2 warning icon or simply save the game then exit. when you reload you may still have high co2 but it will no longer be stuck so you can refresh your air.
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