On the pill and missed my period

I have been trying to conceive for over 2 years. My fiancé and I have not been successful. I had surgery in oct last year for endometriosis, and polysystic ovarian syndrome. After the surgery, my dr put me on depo and a few months ago we decided to try again, and he put me back on the pill. The month before last I missed a pill, but had a period the following week. This last cycle, I did not miss any pills, but did not have a period, but may have possibly had either spotting or implementation bleeding on and off for a day or two, that was brownish. I took two tests that said negative. Anyone have any experience?? I called my dr they may want to do a blood test for hcg levels, only because I have had so much trouble in the past.....could I be pregnant and it's just to early to read?