The corporation said the cases had come to light as part of the BBC's Respect at Work Review prepared with the help of Dinah Rose QC.
It was commissioned when the London headquarters were first engulfed in controversy over Savile's historic sex crimes and their handling of a Newsnight investigation into his behaviour.
The instances were unearthed by a Freedom of Information request submitted by a member of the public.
BBC Scotland's head of public policy & corporate affairs Ian Small said: "We identified two cases relating to harassment involving unwanted attention and inappropriate verbal behaviour. Both cases were investigated and resolved through our existing workplace guidelines."
An earlier version of this story suggested the BBC Scotland cases involved sex abuse. This is incorrect.