The brown discharge is nothing to get to worried about, you just started bc pills, and your body needs time to adjust to the hormones. The first few months on the pill you can experience break through bleeding, or discharge. Once your body adjusts to taking the pill, you wont have that, and your period will also shorten. When I use to take them, if I missed one I would have break through bleeding and when I would get my period it would also be only three days long.