What Causes Brown Secretions?

I am a woman age 24, married 3 months before I suffer from irregular menstrual cycle consulted a doctor and diagnosed cysts ovaries and advised me to reduce weight and gave me Duphaston three pills a day for seven days. Today is the last day of treatment, where I figured secretions brown. Do you believe this cycle?. or what?, because he advised me to take clomid tablets on the second day menstrual cycle