While air conditioning cools and dehumidifies air during the hot summer months, it does not clean air. It may actually contaminate clean air. Room units containing cooling coils that sit outside the window can become contaminated with mold, bacteria and allergens over time. These contaminants can accumulate and spread to the interior of the unit including the blower. From there these contaminants can be aerosolized into your home.
So what can you do? At the end of each season, remove window units and have them cleaned. New filters should be placed in the unit once or twice a season. Air conditioners also create condensation that needs to either evaporate or drain out safely. Check that no water accumulation from condensation is creating a mold problem in your home.