Watery liquid on top of homemade yogurt
We also faced the same problem and found that when the quantity of water is more, the problem persits. The solution is very simple. Boil the milk as long as you wish. (Make sure you dont evaporate the liquid part).  Depending on the consistency of the thickness of the milk, stop the heating and proceed with subsequent steps. 

Also, make sure that the extracts that you add, should have low water content.