Anytime you don't take your birth control as instructed you can cause yourself to have what is called a "withdrawal bleed". It's like a period. Your body on the pill thinks it's pregnant to an extent so you don't ovulate, and are unable to get pregnant. When you stop taking it your body thinks it's time for a period, which is where the withdrawal bleed comes in. When you first start taking birth control you can have irregular spotting even with taking it as directed because your body is adjusting to the birth control. I suggest you start taking it again as directed and do not stop taking it. Additionally for the first week, most pills have in the instructions to use a second form of birth control. As the other poster stated they are not as effective in the first three months, but especially the first week. If you do not want to get pregnant you need to take your birth control every day around the same time, set an alarm if you have to, and use a condom for at least the first week to three months, or every time just as an extra precaution, because birth control is NOT 100% effective.
I would assume it's from stopping the pill. But in order to take birth control pill correctly it is taken for the entire cycle not just around intercourse. Within the first three months of taking birth control pills they may not be effective. Additionally antibiotics and some other medications can cause birth control pills to be non effective.