One possible cause of cysts is too much estrogen. Besides the
estrogen the ovary produces naturally, artificial ones are present
in food, drugs, environmental toxins, etc., and it's believed to adversely affect ovary behavior. That's one of the reasons why birth control pills help many women to get ovaries to work properly again.
There has also been an article stating that NSAIDs like Advil can prevent a normal ovulation follicle from breaking down, leading to cyst formation.