Is It Normal To Have Spotting While Taking Birth Control Pills?

Hi. I was wondering if it is normal to have small spotting while taking the pill. I have been on birth control for about a year now. The other day I missed taking it by two hours. I have intercourse with my boyfriend and lately it has hurt when going in but is okay when I apply lubrication. I'm about two weeks from my period judging by my pills...why am I having tannish discharge. btw it does not hurt when peeing or anything like that. Please help.