My partner has nausea and lower abdominal pain. Is it due to pregnancy or side effect of birth control pills?

Hello doctor,

My partner and I had protected intercourse. I was wearing a condom, and she was on birth control, although the next few days, she took her birth control a few hours late. Also, maybe two of the times I did not wear a condom during the beginning, but I still put one on. She had pain in her lower left abdomen and then spotted for about two and a half weeks straight, but the pain did not last as long. The pain must have lasted roughly for two to four days. After the spotting stopped, she claimed slight nauseousness one morning but did not eat any breakfast that morning and now experiencing pain in her lower right abdomen. We do not know if these are all signs of pregnancy or the results of her birth control taken at different times since they both have the same symptoms, or maybe it is something else. She also had an ovarian cyst that burst a week before the intercourse, but it never leaked. It was about 1.5 - 2 inches. Please help.