First of all, it is normal to have an increase in CO2 in the apartment and bed rooms during the night when your windows are closed.
Only long exposures at high levels of CO2 will create temporary effect such as headaches, nausea, etc. Those effects are felt when waking up, and they can be especially acute for sensitive people. If you're above 2,500 ppm for the whole night, you may start to feel those effects towards the morning.
The best is to measure your bedroom and your children's bedroom to see how high are your CO2 levels. If your bedroom doors are open and your apartment is below 1,500ppm for part of the night/day, it won't cause those health effects.
If your outdoor air pollution (PM2.5) is low, you can open your windows slightly to enable some fresh air to enter your room.
If you live in a polluted outdoor location, the best solution is to ventilate well (full open windows with fans in the house) for 15 minutes during the day and sometimes in the evening if the CO2 levels are above 1,000. Then turn on the air purifiers to the maximum for 20 minutes to clean the air from the harmful PM2.5 particles.
You will notice a much better quality of sleep after implementing those actions.