Issues with Errin?

I just started this birth control two months ago. I was on the combo pill but I suffer from migraines with aura and so I was put on progesterone only. Not going to lie I have been a bit irresponsible and have been 2-3 hours late some days taking the pill. Never actually missing but definitely late. For the last four days I’ve had a bad headache, nausea, brown spotting, exhausted and random hives. I just got off my period three weeks ago but the last three times I’ve had sex with my husband the next day I’m spotting brown the whole day. I’m just frustrated and confused. Anyone have any advice or anything at all!? Thank you