How to reproduce:
1. Create new project
2. Add new Cube gameobject to the Scene
3. Make the Cube a prefab by dragging it to Project view
4. Do it two more times, once a variant, other an original prefab
5. Drag the Cube 1 (other original prefab instance) to the Hierarchy
6. Delete Cube prefab instance in Project view (select Delete Only option on prompt)

Errors:
2021.2, 2022.1
"Problem detected while importing the Prefab file: 'Assets/Cube 1.prefab'.
The file might be corrupt or have missing nested Prefabs. See details below.
Errors:
Prefab instance problem: Cube (Missing Prefab with guid: 6a067e556ce05c5c7885e0bf069a1cfd)

UnityEditor.ProjectBrowser:DeleteSelectedAssets (bool)"

Only 2022.1
"CheckConsistency: Component Transform has PrefabInstance different from its game object 'Cube 1'. Fixing by settings PrefabInstance to None
UnityEditor.ProjectBrowser:DeleteSelectedAssets (bool)"

"[Worker0] CheckConsistency: Component Transform has PrefabInstance different from its game object 'Cube 1'. Fixing by settings PrefabInstance to None"

Reproduced with: 2021.2.0b7, 2022.1.0a9
Does not reproduce with: 2021.1, 2021.2.0b6