Reproduction steps:
1. Open the attached “BugRepro” project
2. Open the “Assets/MainScene.unity” Scene
3. Enable the SubScene for editing in the Hierarchy window
4. Create an empty GameObject in the SubScene (Right-click on SubScene > GameObject > Create empty)
5. Observe the Console window
6. Delete the created GameObject
7. Observe the Console window

Expected result: No errors are thrown
Actual result: “Baking ReferencedPrefabAuthoring!” errors are thrown

Reproducible with: 6000.0.60f1, 6000.2.8f1, 6000.3.0b6, 6000.4.0a3

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