Hemorrhagic cysts?

Lauren • Our second daughter! 👨‍👩‍👧‍👧 EDD 8/8/2016 💕
So it has been 3 weeks tomorrow since I was treated with methotrexate for ectopic pregnancy. My beta hcg is currently at 96 (another draw tomorrow) and I have started having cramping on my left side (ectopic side) that is fairly horrible to say the least and a weird 'sloshy' feeling when I walk around, and discomfort when I get up from sitting or laying down.. I went back to my gp today about it and he ordered an ultrasound, and that's come back that I have several hemorrhagic cysts on both my ovaries and left Fallopian tube. Nothing about the pregnancy, I assume it's too small to see now.. Apparently these ones are quite common but is it at all possible that the original doctor that diagnosed my ectopic, mis diagnosed a hemorrhagic cyst? That's a long shot. And has anyone ever had these and conceived without any dramas? Thanks in advance :)