Could she be pregnant? Yes, as was pointed out above the only way to be 100% sure not to get pregnant is to abstain.

Is she pregnant? Probably not, there are lots of things that can cause a late period, and one of those things is stress. I can't begin to tell you the number of female friends I have that have had unprotected sex then worried themselves out of a period the next month.

If she consistently misses a pill why not switch to something else, such as the patch or the shot?