Especially when we're young, our cycles can sometimes be really irregular. It is even possible to not have a period for two or three months (even longer for some girls) if their periods are irregular. Some girls never have regular ones, others are like clockwork.
This does not mean she cannot get pregnant. In fact, it's worse because you have no way of knowing when she's ovulating. Irregular cycles make having unprotected sex so much more stressful. Use a condom and maybe even a second method, if you can, like the pill. It's about being safe, but it's also about having a less stressful sex life.
If you don't use protection, I can 100% guarantee you guys are going to have another scare and the next time she may actually be pregnant. Wouldn't you rather use a condom and be able to relax and enjoy being together? Or would you rather stress every time she's a couple of days late and end up driving a wedge between you? I know which I'd choose.
Good luck to both of you.