I am on birth control, but I had unprotected sex while on my period the 2nd day of it. The third day it continued like normal, and now it stopped. It only lasted three days. Should I be worried?

Have you been taking your pills as you should? Missed any days? If so that makes higher possibilities of pregnancy...
I honestly recommend you talk to a Dr. or go to a family planning... they can help you with questions and even provide pregnancy test.