Stress can have an effect on your period, even if it is controlled through birth control. The body is programmed to have a period once a month, so a little bit of spotting can be normal, even if it is not time for your period yet.
http://www.drugs.com/seasonique.html This is a good website to look at. It has some good information about the drug and some possible side effects - change in menstral period and cramping included.
Have you tried to contact your doctor? They may be able to give you a more definative answer about continuing your medication or not based on your medical history.