pregnant 2 days after her period stoped

You had unprotected sex at a time in her cycle where she was very fertile, because ovulation happens about five days after menstruation and sperm can live for up to ten days in the body. You can get pregnant after missing one pill, or even after taking the pill but at different times every day. The pills still "being in her system" are not enough protection to make pregnancy unlikely.

If her next period is a week late, I would get a home pregnancy test. If she doesn't want to be pregnant, you should consider getting Plan B One Step from drug stores, Walmart, etc. It's fifty dollars, you don't need a prescription, and it's 89% effective at preventing pregnancy if you take it within 72 hours of having sex. It won't work if she's already pregnant.