What Causes A Missed Period And Brown Vaginal Discharge?

So i had sex on the 30th of november, and im on birth control i have been on it for a while but this week starting sunday i was supposed to have my period around wednesday i had brown discharge and a fleshy substance come out and this happened again thursday and friday, but today was nothing, there was no red blood and im worried, what could be wrong i took a pregnancy test wednesday and the results were neg. but ive never had irregular periods, if anyone has ever had experience or knows anything about this please help we used the withdrawal method plus birth control plus a condom