It depends on how bad it is. The most likely explanation is that your shoes have been exposed to water at some point in their lifetime and the air is causing evaporated particles from this exposure to start falling off. Wiping or brushing away loose particles should solve the problem if your shoes are not too bad, but sometimes a professional might need to fix the issue with glue or other means.
Organizing your closet is also a good idea. If you don't have enough space/shelves for shoes, buy a shoe rack and store them in a place where they won't get dirty.