What Causes Spotting And Stomach Cramps While On Birth Control Pills?

I started bc two months ago and I am now on my third pack. The first month I had dark brown clumps of blood every day but not enough to soak a pantiliner and an extremely light period after 28 days. next month was okay but everyone once in a while I took my pills 30mins to an hour late. In the middle of my second pack I had unprotected sex and my bf came inside of me. But my period cane 2wks later like it was supposed to. 2 wks later (1month after un protected sex) I'm spotting and cramping with dark red brownish blood sometimes clumpy that goes and come. Also my boobs have been sore for an entire week prior to the spoting abs they are now easing up. And I also changed the time of my pills at the start of the third pack and have been using it late but without missing a pill. I've taken many pregnancy tests over the past week or two and they were all negative. Could I pregnant. Is this due to the pills or could it be something more serious.