Could my girlfriend be pregnant?

We had sex about a month ago, a bit longer. She is now 13 days late on her period and complains of consistent, sharp stomach pain, nausea, gurgling in her uterus and ovaries (over the entire month), head aches, a recent acne outbreak on her face and white and brown vaginal discharges. She went to her OBGYN three weeks AFTER we had sex and took a urine pregnancy test, NOT a home pregnancy test and NOT a blood test, which came up negative, but I'm worried that this could have been too early for an accurate test. When we had sex, we used condoms which had been in a hot car for a while, but they didn't break (I explicitly checked) and I did not ejaculate in her when wearing the condom. In addition, she takes birth control somewhat consistently (basically everyday at night, not at the exact same time). She stresses herself out every time we have sex, and nearly convinces herself that she is pregnant every time, and I usually pay little attention to it, though she has never been 12 days late on her period, which is cause for concern. She has recently been somewhat more stressed due to financial issues and such which could be a cause for her late period (her therapist even said her stomach issues were probably from stress), and also her OBGYN informed her that she had a thin uterus lining, which is why she was tested for pregnancy in the first place. I have no idea how she would have gotten pregnant, but the late period and symptoms seem to indicate that she is pregnant. She recently went to the doctor and was diagnosed with stress induced stomach ulcers, which is the cause of the stomach pain, though would this cause her to have a period almost 2 weeks late or not at all? Could she be pregnant? Why would she be getting these symptoms otherwise? Why would her period be 12 days late? Despite the condom and negative test, could she still be pregnant? Please help.