Positive test low progesterone

Hi! This is my first time posting here

This is my third pregnancy, I’ve had one term pregnancy and a miscarriage last summer at 9 weeks. We struggled to conceive my son so this is our first month using Clomid this time around. To my surprise - it worked and were pregnant!

I’m only 12 dpo and my period isn’t due for 2 more days. My HCG has risen nicely from 18 to 40 today. I have hypothyroidism, pcos, insulin resistance, MTHFR and high TPO antibodies. I’m currently under close watch of my OB and endocrinologist. My OB prescribed me premotrium 200mg once a day and I took my first dose yesterday. My progesterone is at 6.

I feel like everything is stacked against us this pregnancy and it’s doomed.

My question is - since starting progesterone yesterday I woke up this morning with spotting that has progressively gotten a little heavier, it is brown and not red so I guess that’s good.

Could the progesterone cause the spotting? Does anyone have experience with super low progesterone and gone on to have a healthy pregnancy?