Reproduction steps:
1. Open the attached project "ReproProj"
2. Open the “/Assets/Core/Scenes/TestScene.unity” Scene
3. In Scene view, fly over the Objects to look at them from above
4. In Hierarchy expand Samples > Box > Scale_1x1x1 > Mesh
5. Select every Prefab in Samples > Box > Scale_1x1x1 > Mesh and in Inspector click “Execute“ button
6. Repeat step 5 for every Prefab in Samples > Box > Scale_1x1x1 > Primitive
7. Repeat step 5 for every Prefab in Samples > Box > Scale_4x4x4 > Mesh
8. Repeat step 5 for every Prefab in Samples > Box > Scale_4x4x4 > Primitive
9. Repeat step 5 for every Prefab in Samples > Box > Sector
10. Observe Scene view

Expected result: Prefabs do not exist in the Scene view and are disabled
Actual result: Some Prefabs are still present in the Scene view

Reproducible with: 2022.3.60f1, 6000.0.42f1, 6000.1.0b9, 6000.2.0a6

Testing environment: Windows 10 Enterprise 21H2
Not reproducible on: No other environment tested