Thanks for consulting us.
This pain could have many origins, like a threatened miscarriage
or it may be related to your ovarian cyst or an undiagnosed heterotropic pregnancy, or it could have an origin from any other abdominal organ like urinary tract
(e.g. due to stones), Intestines (e.g. diverticulitis
I suggest you should have a repeat trans-vaginal ultrasound
from a tertiary ultrasound center along with an ultrasound whole abdomen & a urine DR to exclude stones.
Wish you good health.