Why was one of my ovaries removed when my pathology report stated that the cyst was in fact benign.my ovary appeared unremarkable and was functioning.?

Ask your MD: There are a lot of factors like the size or how much of the ovary was involved in the cyst. Only your md will be able to answer your question.

Cystic Lesion: Sometimes lesions (of any organ) are removed for concerning signs/symptoms (esp. On imaging) for malignancy. This approach may save the life of someone where it was indeed malignant (only pathology gives this info), however, in other cases may lead to the removal of a benign lesion. Medical research continues to look for better ways to know this before, but that's the best approach currently.