Periods and pills

I've been on the progesterone-only pill for about 5 months. This means I still get periods every month but I'm still on birth control. My cycle is normally very regular.
About 4 weeks ago I missed a pill but I had sex the next day so I then took the emergency pill. My period came a week after that, when it was supposed to, but it was very very light which was different. 12 days after that period I had a random period which has been going for 12 days now (moderate bleeding). Sometimes it stops for a day so I think it's over but it comes back the next day.
Anyone ever experienced something similar or have any suggestions of what it may be?
I have done 3 pregnancy tests done since the emergency pill and all have been negative.