My Boyfriend And I Were Recently Treated For Chlamyidia. He

My boyfriend and I were recently treated for Chlamyidia. He had to take a version which didn't have amoxicillin and I took one that did. It was a one time dosage that was taken by mouth. (Two pills in each bottle) We had to wait a week after taking the pills to have sex and we waited an extra day even. Now almost 2 weeks later I have been noticing an odd dark brown discharge, not anything like my period though. Everytime I go to wipe off and I notice it and last night I noticed that it was in my underwear when I woke up. Any idea on what this could be and is it dangerous. I should also probably mention that he isn't having any weird symptoms and we have had unprotected sex since that week was up a couple of times. I also got the Nexoplan injection in my arm about a month ago. The discharge smells bad.