Period + birth control

Hello, I just recently start birth control. My gyne told me to start my pill pack the first day I start my period so I did. My period usually lasts 4-6 days but I am going on day 12 of my period (& day 12 of my pill pack). I thought I was off of it today so my boyfriend and I had sex. I bled again and my discharge that is usually white/milkey around this time was dark grey, almost black. I am very concerned something is wrong with my body   And if it is just my body adjusting to the new medicine, will I get my period again when I'm supposed to on the pill pack? Or will I be late