Reproduction steps:
1. Open the attached “BugRepro” project
2. Open the “Assets/Scenes/SampleScene.unity“ Scene
3. Open the “CubePrefabOuter” prefab in prefab mode (click the Arrow to the right of the prefab instance in the Hierarchy window)
4. Drag the “SpherePrefabInner Variant” from the Hierarchy window into the “Assets/_Prefabs” folder in the Project window
5. In the popup dialog, select the “Original Prefab”
6. Observe the created prefab in the “Assets/_Prefabs” folder

Expected result: An original prefab is created
Actual result: A prefab variant is created

Reproducible with: 2022.1.0a1, 2022.3.60f1, 6000.0.51f1, 6000.1.7f1, 6000.2.0b4

Reproducible on: Windows 11
Not reproducible on: No other environment tested