Can Taking Birth Control Pill During Pregnancy Affect The Baby ?

I hope someone can help. I m 30 years old and was just diagnosed with PCOS in March of this year. My doctor told me for the pain that I can take up to 4 ibuprofen for pain. I told her that my fiance and I were ttc. She seemed to ignore it. This month I decided to put of ttc and go on the pill. I was prescribed Desogen. I got my period this past Sunday and started the pill. It s normal for me that when I get my period, I spot for the first day, day and a half, then I m really heavy for about the next 2 days (changing super plus tampons every 1-2 hours). Then my period gets lighter and lighter. I barely had any spotting. I called my doctors office on Tuesday and was basically told that the pill should not have affected me that quick and that once I get to the inactive pills that I might want to take a pregnancy test if I still don t get my period. About 2-3 days before my period, my breasts get sore . This time they are so sore that I fell asleep on my stomach the other day and when I woke up and moved, I cried because they hurt so bad. They have never been this sore ever. Should I take a preg. test now and stop the pills or wait like the nurse told me. I have posted this on other forums with no answers. I just finished the first week of active pills. I have been on the pill in the past but never missed a period when I have started them. I m Scared! Any advice will be greatly appreciated. Thanks