What Causes Brown Vaginal Discharge After Having Protected Sex?

I am on the pill for about 4 months now. Before the pill my periods have came every 3 weeks on the dot. yesterday i thought i started my period. Then there was some brown discharge. I couldn't tell if it was old blood or what but there wasn't a lot. Also this past month I have forgot pills so the next day I would take them. I ALWAYS use protection too when I have sex. What does this mean?