brown discharge

I was on Mirena IUD for 3 yrs out in July, went on Progesterone pull (Errin) for a few months after and eventually stopped in September. It's now December and my periods have been weird. There's always been brown spotting beforehand and this time it's late by 3 days (pregnancy test came out negative this morning) and I have small amounts of brown blood. I always seem to have a lower backache and I just hope this is all a result of my body just taking a really long time to readjust without hormones instead of endometriosis or something. I never had brown spotting before I had the IUD and since I'm (probably) not pregnant, I'm just a little concerned.