Before you can begin to tackle the problem of the smell from your ducts you have to determine what might be causing it. Mold. One of the most common causes of a musty smell in ductwork is the presence of mold in an air conditioner. The mold will grow on both the condenser coils and in the collection pan. The ductwork. Another common issue could be with any of the ductwork that runs through a crawl space beneath the house.