Missed period but had spotting

Ever since I have gone back to college for the semester I have yet to get my period, I am now over a week late. I have had spotting twice this month for around 3 days each time but no period. My boyfriend and I are very good at being safe when we have sex, so I find it hard to believe I could be pregnant but I'm getting worried that I am. Although I have been exercising a lot lately since I am a d3 athlete and I've been doing a lot of running and since I haven't had my period since before I came back to school, could I be missing it because of all the exercising? Or could I be pregnant?