When checking Revit Family files back into Vault and ticking the 'Delete working copies' option, Vault should also delete any backups of the Family files too. e.g. Family.0001.rfa, Family.0002.rfa
Leaving the backups for the Revit Family files .RFA in the folder not only makes a mess in that folder, but the user has to manually traverse into the folder and delete them.
Either delete the backups automatically or provide the user an option to do so.