implantation bleeding

I went in to the drs on Monday bc I started what seems to be my menstrual cycle but I also had taken pregnancy test and they were positive. Sunday night AF came by but I had a horrible headache and I had vomiting, I rarely get sick n this is why I decided to call the drs office n bc I had been told that I have issues with my eggs and would b rare/difficult to get pregnant on my own... blood work was abnormal and hospital pregnancy test was one positive and one negative. He examen my cervix n my uterus and everything seems to be fine. He said not to count this as my cycle and to wait about 2-3 months to start with my fi st fertility treatment, clomid. I'm soo confused to what happened to me as the dr couldn't say what was going on.