doctor said she may be pregnant even though she is on her period

Hey guys my girlfriend and I have been super worried that she is pregnant we usually have unprotected sex (I know it's bad but it's just what it is we have learned our lesson) and We have been afraid. At first she wasn't getting her period for 5 days and was feeling nauscious in the mornings. she took a test and it said No but still no period. She went to her nurse and asked for virth control pills while she was doing that she got her period and the nurse said perfect you should start taking it today. Before she even took her pill her period stopped and was clean. She took the pill and her period stopped for the day and a half, although she was still showing sign of cramps and tender breasts. When her period came back, now 3rd day on birth control she decided to go to a clinic bcuz she does not have a family doctor. Anyways the doctor said she maybe pregnant even though she is on her period and I just want to see what you guys have to say. Thanks