She should check in with her ob-gyn about the symptoms; in addition to all the above possibilities, it might also be that her pills themselves are making her ovaries ache. Talk to the doc. :)
She has had sex only 2 times, both being not with me, but she was using condoms and is now on the pill, for a month or two, and I doubt it was trasmited by the partner unless it can stay dormant for so long.
Could be ovarian cysts. Also sharp pains that are so strong you can hardly even sit down are common with appendicitis, and ectopic pregnancy, both of which are time-sensitive so she shouldn't be waiting around. I think you can get some bad aching with pelvic inflammatory disease. Possibly you need to provide the doctor a little more information, such as whether she is sexually active or not, whether she has always practiced safe sex, whether she could possibly have been exposed to anything transmitted by a partner, and so on. If she has seen a general practitioner and not an ob-gyn, she should see an ob-gyn. Good luck!