at a guess I'm assuming that they don't use c02 scrubbers, because every replicator on the ship, dozens to hundreds of them placed for convenience can release fresh air into the ship which still makes you wonder what happens to the bad air? And for what doesn't get topped up naturally, the main transporters probably pick up the slack.
The don't clean the ship, and by the middle of season one tng, no one knew what a nanite was.
Cleaning and air supply has to be done magically.
How do they release the neurozine gas?
Whattabout Geordie and Bev trapped in that cargo bay in The Disaster?