Did birth control protect me ?!

Patient : Hi my question is well I'm on the birth control junel low estrogen, this is my first month taking it I never missed a day or nothing one day my exboyfriend & I had sex & he had ejaculated inside of me than I started cramping through out the day well the next day I was at work & all of a sudden I got my period but I was still on my active pills I kept taking them almost every time i always take my birth control at 9;40 am I forgot around 9;40 one day & took it around now 10;40am, I was wondering even though I caught my period while I was still on the active pill was I still protected from getting pregnant? I've read people can still get pregnant while on the pill it's 99.9% effective .
Symptoms:  Sore breast , cramping, back pain & nausea, increase in appetite , mood swings & tiredness
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