Help!

So I've been taking birth control for months now. My periods have been regular. I have missed some pills but not by much. Maybe couple of hours. Anyways my boyfriend and I have sex and he may or may not have came in me. He tried to pull out but We don't really keep track if any gets in me. Anyways, last Saturday was the last day I had my period and today (Sunday May 8th) I started bleeding but it's like brown and it isn't a lot at all. At first it was light red and now it's brown. Anyone know what could be happening???