I know exactly what you are referring to. Your'e doctor is right, it is common, and according to my aunt in NY, her doctor told her it is actually hardened mucous deposits. Sometimes after having a cold or sinus infection, you'll notice them, and they do make a person's breath smell horrible too.
Better out than in if you can dislodge them. Oil pulling may help you. I oil pull every morning with just enough oil to fill the bottom of a small dixie cup. Swishing the oil in the mouth for a few minutes after brushing your teeth does have a "pulling" effect and will often pull up mucous clumps from deep within the throat that gargling won't pull. In the past, I 've pulled out some of these "stones" when oil pulling.
To get to the root of the problem, try to eat less mucous forming foods, and get more vegetables and fruits in the diet. Dairy is often mucous causing.