Menstruation Question - Brown Discharge

I want to give a little background info because I found a lot of other people are posting that they're in similar situations but I'm seeing conflicting responses to their posts.
I lost my virginity in early July. Been having sex regularly usually using a condom. My pd is usually very regular and on time. In July it was due the week I started having sex and came right on time. My period in August was worrisome because I had unprotected sex the day it was due. Then it didn't come. I panicked and took an emergency contraceptive 3 days later. My period came about 3 days after that and lasted longer than usual.
My September period is 2 weeks late, almost 3 weeks. I took 2 pregnancy tests and they're both negative. Tonight I found brown discharge in my underwear. I'm worried and dont know what this could mean
Could my pd be irregular simply because I recently lost my virginity and that somehow affected my cycle? Or has the emergency contraceptive messed my cycle up making me almost 3 weeks late this month? Or should I be seriously worried about possibly being pregnant?
Please help my boyfriend and i are so worried