Hi, I'm an anon. user, and I just came across your post. If you are really worried have her take a pregnancy test again. Some pregnancy tests do not work properly due to it being damaged in poor packaging, or some kind of damage during the making of the product. I highly advise you have her retake.
But another cause could be a hormonal imbalance, but just because there is a slight chance that she could have an imbalance does not mean that it is just that. Women have different periods. Some girls can go three to four months with out having a period, some can go twice in a month. You should talk to her about how many times she gets her period just in case as well. And if you hadn't used a condom and you cummed the chances are all the more likely.
You don't want to wait. Have her immediately take another test.
Her frequent belly aches and going to the bathroom could be due to some upset with her stomach.
But once again, have her retake the pregnancy test. Do not take the signs lightly.