Reproduction steps:
1. Open the attached “UnityBugProbuilderScenesCheckout.zip” project
2. Make sure two scenes “OutdoorsScene” and “New Scene” are opened in the Hierarchy
3. Set the “New Scene” as the Active Scene (Right click > Set Active Scene)
4. Duplicate the “Cube” GameObject in the “New Scene”
5. Observe the Scenes in the Hierarchy

Expected result: Only “New Scene” is marked as dirty
Actual result: Both "New Scene" and "OutdoorsScene" are marked as dirty

Reproducible with: 5.1.0 (2021.3.41f1, 2022.3.40f1), 5.2.2 (2021.3.41f1, 2022.3.40f1), 6.0.1-pre.2 (6000.0.0b14)
Not reproducible with: 5.0.7 (2021.3.41f1, 2022.3.40f1)
Fixed in: 6.0.1 (6000.0.13f1)

Reproducible on: Windows 10 (User reported), Windows 11
Not reproducible on: No other environment tested