Watery liquid on top of homemade yogurt I made homemade yogurt tonight, except it didn't turn out as I expected. I followed this recipe with a few exceptions.

I made it with three quarts of milk instead of 4 (or two). I modified the amount of "culture" I used accordingly.

I also added flavorings after the milk had cooled and the new culture extracted. I added some lemon juice (thought it was lime, mixed up the bottle). And added some Jelly Belly Green Apple Syrup for icicle pops or something.

I also put it in 8 oz jars instead of 32 oz jars.

The jar with the new culture/start in it, turned out fine. Nice and solid. However, the other jars are about half liquid and half solid. Did adding an acid (lemon juice) mess something up? Is this expected?

What do I need to do next time to make sure this doesn't happen. I haven't tasted it yet so I don't know if it's good or not.
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.