What Causes Brown Discharge After Taking Contraceptive Pills?

I missed my last two active pills in my pill pack. Thursday and Friday. I was supposed to start my period Wednesday.I had all the symptoms of PMS but it never came. I started my new pack of pills yesterday. I woke up with brown discharge this morning like I sometimes get after my period is over. Should I be worried about being pregnant? I also took 2 tests that came back negative