Reproduction steps:
1. Open the attached project “Broken Baking”
2. Open the “Assets/Scenes/SampleScene” Scene
3. In the Hierarchy window select the “Subscene” Subscene
4. Make sure the “SubScene” Subscene is not open (the checkbox is unticked)
5. Open the Preferences window (Unity > Settings for macOS, Edit > Preferences for Windows)
6. In the Preferences window open the Entities tab
7. Click on the “Clear Entity Cache” button
8. Click “OK” in the pop-up window
9. Reload the domain (Tools > ReloadDomain)
10. Click on the “Clear Entity Cache” button again
11. Observe the Console window

Expected result: No warnings or errors are shown in the Console
Actual result: Warning “[Worker2] The referenced script is missing on Cube (index 1 in components list)” is thrown in the Console

Reproducible with: 2022.3.10f1, 2023.1.16f1
Not reproducible with: 2023.2.0a8, 2023.2.0b13, 2023.3.0a9
Couldn’t test with: 2021.3.31f1 - Unable to downgrade the Editor version due to the project's specific package dependencies,
2023.2.0a1 - 2023.2.0a7 - Couldn’t test, due to incompatible package dependencies versions

Reproducible on: macOS 13.5.2
Not reproducible on: No other environment tested