Don't worry, I think you two are just noticing things that happen normally and you just didn't notice them before. Girls often gain a little bit of weight (especially in their breasts) before their period. The smell and taste of your vaginal fluid (and semen) can change even just depending on what you ate last! Also, if she is stressed out right now, that is probably why her period was late.
If she was pregnant she would have missed her period entirely and for much longer and there would have been other signs. If her period is late again it is also probably just from stress.
Please do, however, use a condom when you do have vaginal sex and she can definitely ask her doctor about birth control (it also helps with cramps, if she has bad ones). Just keep your semen (including pre-ejaculate) away from her vagina and you should be fine.