Steps to reproduce:
1. Create new Unity project
2. Create new Scene in Project window (Create > Scene > Scene)
3. Install Entities and Entities Graphics package via Package Manager
4. In Hierarchy create a New Sub Scene
5. Select “New Sub Scene” GO in Hierarchy window
6. In Inspector window > Sub Scene Component select “Scene Asset”
7. In “Select Scene Asset” window select “New Scene” Scene
8. Open “Select Scene Asset” window select “New Sub Scene” Scene again
9. Observe the Console window 

Actual results: Error is thrown in the Console “Destroying GameObjects immediately is not permitted during physics trigger/contact, animation event callbacks, rendering callbacks or OnValidate. You must use Destroy instead” after selecting “New Sub Scene” Scene again

Expected results:  No errors are thrown in the Console after selecting “New Sub Scene” Scene again

Reproducible with versions: 6000.0.66f2, 6000.3.8f1, 6000.4.0b8, 6000.5.0a6

Tested on (OS): macOS Silicon Tahoe 26.2 (M1)