If you were deficient in magnesium, then your body grabbed the magnesium and it didn't create the 'great clean out' of your intestines.
It is also possible that you have parasites, which can block the ducts in the liver and prevent the stones from coming out. You should probably do a parasite cleanse before attempting another LF.
Also, did you see any chaff? Sometimes people just get chaff the first time and then stone on later LFs.