How to reproduce:
1. Open the attached “IN-138736“ project
2. Open the “SampleScene“ scene
3. In the Hierarchy window, if not opened, open the “Test Subscene“ subscene (Checkbox near the “Test Subscene“) and expand it’s contents
4. In the Hierarchy window, open the “TestPrefab (Grey Cube)“ in Prefab Scene Edit mode (Arrow to the right of the GameObject)
5. In the Hierarchy window, select the “Red Cube“ GameObject and disable it from the Inspector window
6. Observe the Game view

Actual result: Some materials on the Prefab’s GameObjects have moved to other GameObjects in the same Prefab
Expected result: Materials on the remaining active GameObjects in the Prefab did not change

Reproducible with: 1.4.8 (6000.0.58f2), 1.4.18 (6000.3.12f1), 6000.4.1f1, 6000.5.0b2, 6000.6.0a2 (64de5ee3637)
Not reproducible with: 1.0.0-exp.14 (2023.3.0a2), 1.4.7 (6000.0.58f2)

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

Notes:
- Issue does not reproduce in Play mode or Player if the child GameObject (Entity) is disabled with a timer through a script
- In the Scene view, the GameObject gets disabled correctly and no materials get moved. This is different from the Game view, where they are moved
- Issue exhibits non-deterministic behavior as sometimes the wrong GameObject is disabled instead of the Material shuffle