What Causes A Monthly Cycle In The Middle Of A Birth Control?

i have been on my monthly cycle for 13 days now. i had a baby 9 months ago and have been back on birth control since. this cycle started in the middle of my birth control and that is not normal (i don't think). i have recently been to the dr. due to pain in my back on my left side and lower abdomen area and i had a ovarian cyst and a kidney stone on my left side i am a little concerned that with these recent symptoms there may be something more going on.