Period ovulation ect

Okay so my partner and I had sex all through my fertile window and a bit before that, I was sure I would fall pregnant this cycle it's our first time trying since having a partial molar in May, 
To my surprise period arrived Monday when she was due to, I have had more cramping then usual and now i felt like I was about to throw up everywhere mind you period flow has gotten lighter, my ob said that you can still have a period the first three months of pregnancy my question is has anyone had this happen? 
I was swearing I could see second lines on the hpt but I think I wanted it that bad I was seeing it or indent lines ect only other thing could be a chemical  pregnancy but ob said no. Help please!!