Thanks for the query.
pills can cause side effects like inter-menstrual spotting, increase vaginal discharge
If the vaginal discharge is not associated with smell or itching, no need to worry.
Regarding the brown discharge, it could be a side effect of the pill. And possibly this will subside soon.
You once go for ultrasound
and physical examination which will rule out other causes of spotting.
For more details you can ask me through: http://www.healthcaremagic.com/doctors/dr-sree-gouri-sr/63429