Hello there You said you are on pills so i would want to know which kind of pills. As if its only progesterone containing pill then it can lead to absence of periods. But combined pills which contain both estrogen and progesterone regualrize periods. If your pill is combined one, i guess you are not taking them regularly and on fixed time and so you have irregular periods. Coming to brown discharge you have it might be because of the vaginal soreness you have. Especially if vagina is dry and sore there is likely chances of getting abrasions (cuts) while having intercourse which can lead blood stained brownish discharge. The soreness could also be due to you the pill if it contains only progesterone. Besides for irregular periods you should get an ultrasound and meet up a doctor personally who can examine you and advise further tests accordingly.