Carbon dioxide
Your duplicates quickly consume all the oxygen in the colony and replace it with carbon dioxide. You already know how to get more oxygen, but that doesn't prevent this incombustible natural gas from building up.
The first thing you should know is that carbon dioxide (carbon dioxide) is a heavy gas and settles below oxygen. If there is not enough oxygen, carbon dioxide will gradually build up. First, make sure your colony has multiple levels.
Next, you need to do some research and open the Air Scrubber. It can be found in the research section "Liquid Piping" - "Percolation" - "Advanced Filtration". This device uses water to remove excess carbon dioxide air, and in return it will produce polluted water. You can use a water purifier for filtration and reuse to minimize waste.
You can also convert carbon dioxide to a liquid or solid with a thermostat and then store it.
Contaminated oxygen
Typically, dirty oxygen is generated whenever there is dirt, mucus, or contaminated water nearby. Toilets, bio-distillers, composts and air scrubbers also contribute to pollution. If you have too much air pollution, your duplicates will get sick.
You can get rid of it with an air deodorizer. It can be found under "Liquid Piping" - "Sanitation". The deodorizer requires a filter (sand) to filter out airborne contamination.
This is extremely convenient at first as you expand your colony, but once you start running out of resources it may not be the best solution.
You can also use a thermostat to cool the dirty oxygen and then turn it into heat.
Hydrogen
Over time, hydrogen may appear in your colony. This is especially true if you are using an electrolyser to produce oxygen. Since hydrogen is the lightest of all natural gases in the game, it will rise upward with a pinkish tint. It is important to remove the Hydrogen as soon as you notice its presence, because it is a refractory gas that lowers the temperature.
You can easily remove it with a hydrogen generator. These handy devices use gas pumps to absorb hydrogen and convert it into energy that you can use for other machines.
Place the electrolyzer and hydrogen generator in a separate room where you can direct oxygen and hydrogen to their respective locations without worrying about contaminating the colony with hydrogen.