Hi,
Welcome to ehealthforum.
The continued spotting could be due to the infection, the ovarian cyst or even pregnancy. You should consider visiting your doctor again to have repeat examination and get a blood HCG test done along with ultrasound scan to confirm/rule out pregnancy and look into the current status of the ovarian cyst. Get started on appropriate treatment as indicated. Get your partner treated simultaneously and avoid having intercourse while being on treatment to prevent re-infection.
Take care.