Do an enema. The stones can get caught in the intestine if you are have a lot of mucous, fecal matter, etc....

Also, if you can do p&b shakes, you'll find that they scoop up stones that you don't pass. When I do the shakes, I do 3 the day I'm passing stones, and I always have bowel movements with stones all in them. So, cleaning the small intestine and colon are very important so that you don't get re-circulating toxins that make you feel about 10 times worse.