Stomach ache, head ache, late period, negative pregnancy test?

We had sex about 5 weeks ago, and she is now 9 days late on her period. 3 weeks after we had sex, she took a urine test at her OBGYN office and it came up negative, NOT a blood test and NOT a home pregnancy test. Could this have been too early for an accurate test? When we had sex, we used a condom that had been in a hot car for a few hours, but it didn't break (I explicitly checked) and I did not ejaculate in her either. She has been complaining of consistent and intense stomach pain as well as head aches and nausea. She complained also of brown and white vaginal discharge. In addition, her OBGYN said she had a thin uterus lining, which is why she gave her the pregnancy test in the first place (which came out negative). Could 3 weeks been not enough time to get an accurate test? Could the thin uterus lining cause her late period? Also she scares herself into being pregnant every time we have sex, but her period has yet to be 9 days late. Could she be pregnant? How would she have even gotten pregnant also? If we used a condom (even one that had been sitting in a hot car), that did not break, and I didn't even ejaculate in her how could she have gotten pregnant?