Brown discharge but on birth control?!

Okay I'm worrying myself to death right now. I've been on birth control for 2 months now and I missed my period the first month but got it the second month, and last month there was one day I accidnetly missed the pill but made sure to take 2 the next day, and I also forgot to take my last placebo pill of the month. My boyfriend and I usually have protected sex but there was one incident he came inside me, and this was also the day I didn't take my last placebo pill :/ I ended my last period about a week ago, and when I got home today there was a HUGE brown/red stain on my underwear with a weird smell. My pee is 100% clear and when I wipe it's also clear. The discharge is still going on but much lighter and it looks like a very light brown/red color. What could this mean??