There may be notes with the same name, but with different card hierarchy.
Software - Note Taking - Supernotes - Bugs - FRs - Misc - Some Other App - Bugs - FRs - Misc etc
And when you fire the ‘Add Parent/Link’ popup there are just several Bugs, Misc and FRs cards. And there is no way to find which on do you actually need when creating Parent/Link.
I suggest to add Card Hierarchy to the ‘Add Parent/Link’ popup list for the cards which name is not unique.
Note Name Something useful Bugs (Software>Note Taking>Supernotes) Another note Bugs (Software>Note Taking>Some Other App) etc