Could my girlfriend be pregnant?

My girlfriend and I had sex a little over a month ago. Since that date she has been experiencing stomach pain along with nausea and head aches. She is also 9 days late on her period now. When we had sex we used condoms that had been sitting in a hot car for a while, but it did not break (I checked explicitly). In addition, I did not ejaculate in her and rather pulled out before doing so. Again I checked and the condom did not break, I made sure of it. About 3 weeks after we had sex, she went to the doctor and had a urine pregnancy test, which came out negative. The doctor said that her uterus lining was thin, which might have caused a very light period, or none at all. However, this might have been too early for a true answer. She also complained of some brown and white vaginal discharge. She claims that the brown discharge was dried blood, which could have been spotting, or an incredibly light period. She has only been experiencing stomach discomfort and head aches since about a month since having sex, no breast swelling or darkening of the nipple. We practiced safe sex, but still I am worried that she could be pregnant. Please help