What Causes Brown Vaginal Discharge While Having Ovarian Cyst?

hi, I just would like to know if this is normal. I'm having brown discharges for a week now even if my menstruation is already over. I also got this before I had my menstruation. my pregnancy test reaveals that I am positive but when i had the transvaginal ultrasound, The doctor said that it might just be physiologic or pathologic and there is no placental sac noted. she found cyst in my left ovary but she said it might be because my menstruation is about to come.I had my menstraution last week. i hope you can answer my questions.