Isn’t there a line about how Blue Fairy only grants wishes to those whose hearts are true? Could be a call back to when Belle said that Rumple’s “heart is true” in The Outsider.
Perhaps when she was the Miller’s daughter, Cora asked the Blue Fairy for help to escape her life. However, the Blue Fairy refused to grant Cora’s wish because Cora’s heart wasn’t true. Then along comes Rumple. Eventually after making the deal with Rumple, Cora is in a position of power when she meets Eva. Despite being royal, Eva has had a wish granted by the Blue Fairy. Enraged by how unfair that is, Cora takes it upon herself to destroy the thing Eva loves most (Snow) and see to it that Regina becomes the queen.
All magic comes with a price!
Keeper of Felix