Steps to reproduce:
1: Create new project
2: Create GameObject A in the hierarchy, make it a prefab
3: Create GameObject B in the hierarchy, make it a prefab
4: Drag prefab A from the hierarchy onto prefab B in the Project Browser, in the Popup Select "Replace Anyway", then Select "Prefab Variant"

Expect result: Prefab B is now a variant of A
Actual result: Prefab B is an original prefab.