Reproduction steps:

1. Create a new project
2. Create 2 GameObjects: Cube and Sphere
3. Drag both GameObjects to the Project Window to make them Prefabs
4. Make the Sphere GameObject a child of the Cube GameObject in the Hierarchy window
5. Drag the nested prefab into the Project window
6. Click “Prefab Variant” in the pop-up that appears
7. Undo (on Windows Ctrl + Z, on macOS CMD + Z)
8. Redo (on Windows Ctrl + Y, on macOS CMD + Shift + Z)

{}Expected result{}: No errors are thrown

{}Actual result{}: The following error is thrown:
{code:java}
Component Transform has PrefabInstance different from its game object 'Sphere'. Fixing by setting PrefabInstance to None
UnityEditor.EditorApplication:Internal_CallGlobalEventHandler () {code}
{}Platforms tested{}: macOS Monterey 12.6, Ubuntu 20

{}Note{}: Also reproducible by using the Context Options (Edit > Undo/Redo)