What Causes Irregular Period While On Birth Control?

My doctor just put me on a new birth control, Low-Ogestrel and told me i could use it just like Seasonique because i informed him that was my preference. He instructed me to take the sugar pills out of the first three packs and take them daily as normal. Ive never had an abnormal menstrual cycle until now. I'm within the third month of taking this particular birth control and I've started my period over 2weeks ago, this beginning my 3 week. Im unsure of what to think or even where to begin. What could be wrong with me?