I don't believe that anyone on the internet can determine exactly the cause, you would have to see a doctor to be sure. I'm not very clear on when and how long you were on birth control? Birth Control Pills require the person to take the pill for 21 days and then stop for seven days (during which time, there is a breakthrough bleed, not a period) before continuing the cycle again. Is there a reason, you were on birth control for 13 days? I don't believe you were ever pregnant from what you say here. You took the morning after pill less than 24 hours after and you had been on birth control. Conception may not even have occurred after 5 days, it would have been too soon for you to even tell if you were pregnant. Personally, from the information you have given I think it is probably just a side effect from not taking birth control pills the way you are supposed to. But I am not a doctor, that is just a guess.
Also, I know that birth control can be a pain to remember etc. but if you miss one or more there is a 7 day rule. i.e. Do not have unprotected sex (i.e. without a condom) until you have been taking the birth control properly for seven days.