There are several different causes of ovarian cysts. Some of these do require medical intervention and workup, as your girlfriend's doctor
has evidently decided. Discussing this issue in detail with her OB / GYN doctor is very important.
In young women, the most common cause of ovarian cysts is simple a normal variant of the cysts that form in the course of the ovulatory cycle. However, these can sometimes get quite large, can rupture and / or can cause significant pain. In other words, even a 'normal' cyst is not normal if it causes problems. Large cysts can sometimes need to be removed because they create a risk that the ovary can twist on itself and strangle its blood supply (ovarian torsion). Occasionally the can also impair the ability to get pregnant.
Rarely, a cyst can be a sign of a tumor, either a benign tumor or an ovarian cancer. Sometimes, these tumors need to be investigated closely to determine whether they need to be taken out or otherwise treated.
As always, the diagnosis and the management of your girlfriend's particular condition can only be done by the doctor who has performed her physical examination personally and who is managing her care. Any concerns and questions are best directed to that doctor.