What Causes Pain In The Ovaries After Taking I Pill?

Hi, my girlfriend and I had sex a few days ago and the condom unfortunately split. This occured around 11:00pm so we went early the next morning to my GP up the road to get the pill. She took the pill under 12 hrs of the sex. The problem is she was within two days roughly of her period when the unprotected sex occured. Her ovaries have been hurting since the day after the sex and her period has not occured. That said, I know the pill causes irregularity in a women's period cycle. Why do her ovaries hurt is the main question and can you provide some assurance?