It is possible that the endometrial preparation has become inadequate and hence you have had only some spotting. If you have never missed the any of the pills, pregnancy
is very unlikely. In the current scenario, you should see a specialist for a complete clinical assessment and get a trans-vaginal sonogram along with a blood test
for pregnancy. Urine pregnancy test is of not much use in the current situation. Your migraines may not be related to pregnancy; they may be pill-related. Hope you find this information useful. Wish you good health.