I am so sorry to hear about your cancer. I would follow your gynecologist's recommendation and get the ultrasound in 3 months. It is unlikely you are facing two different cancers. But, it is possible for the rectal cancer to spread to the female organs. But, usually, you would see more widespread signs of metastasis, rather than just an ovarian cyst if the two were linked. The same virus that is implicated in causing most cervical cancer is also thought to cause most rectal cancer. So, keeping a close eye on the cervix and ovaries is important. You should also continue to get regular pap smears. Ovarian cysts are very common and odds are with you that it is a benign cyst. If you continue to get the recommended checks on time, then you will catch any changes early. My thoughts and prayers are with you for healing!
Shelly