You must have airflow on, setting it to recirculation will trap damp air inside car and cause your problem, make sure you don't park the vehicle like that also.
The air-con simply collects the moisture in the air as it passes over the matrix, it then freezes it and it builds up like in an old freezer, when you shut down the ice melts and should exit to outside via a drain, often the drains get blocked with gunge and the whole thing starts to smell as the gunge gets worse. A good garage service should clean those drains.
The Air-Con does not clean the air , (only chills it), however you may have pollen filters in the air intakes, they should be changed every year.
Recirculation is good if you want a quick warm up but you must open it again to let fresh air in once your at running temperature. If you were to do a long trip with recirculation on you will become drowsy due lack of fresh oxygen in the car.