My great-grandmother was born Frances Iona Rampley. There is only one record on her that uses that name: her birth certificate. Her marriage record, mortgages she signed, her social security death index entry, 1900-1940 census enumerations, court documents, estate papers, tombstone, etc. all list her as Fannie.
Your ancestor may never have used their "real" name. And if they never used their "real name" was that their real name? In the case of my great-grandmother, I list her as Fannie and in my notes indicate what her record of birth says.