The morning after pill will prevent a fertilized egg from adhering to the uterine wall - and is flushed away - this happens many times, even without the pill. Uterine insufficiency can prevent any fertilized egg from embedding itself on the uterine wall, and therefore, the egg is not carried to term. This can happen for a number of reasons - usually the hormone "progesterone" is involved.
Based on your description, the woman would not be pregnant. Most pills work within 72 hours after intercourse and the periods go to show that fertilization did not take place. If you have any suspicion, the best way to find out is by taking a test.