3 days late on period but on birth control?

Patient: Hi! I had sex on September 6th and he did ejaculate in me I was about 4 days into my second pack of birth control when that happend. I have not missed a day both month. I was supposed to get my period on the 25th it is now the 28th i’ve had extremley light bleeding its pretty much only there when I wipe or a drop in my underwear and now I am having brown discharge. What is happening?

Doctor: