Pregnancy Doubt. And negative later?

We are recently married couple(marriage in february). We have checked the pregnancy of my wife during July and it has shown two lines on the strip and as we consulted doctor next day, they confirmed the pregnancy and told that she was two months pregnant by then. They informed us to take a scan and other tests during third month. Due to some reasons, we couldn't attend for tests in third month. Instead we went to hospital in fourth month. To our astonishment they told that pregnancy was not there. We took UTP, ultrasound and other tests to confirm that. All tests showed a negative result for pregnancy. And the doctor informed that my wife has PCOD issue. Actually she has obese body since long and even when she has undergone tests for thyroid and pelvis ultrasound scan one year ago, there is no sign of PCOD at that time. We couldn't be able to notice what has gone wrong here? Why the pregnancy has shown positive at first and negative later? Please tell your valuable opinions. Thank you.