How to reproduce:
1. Open the user's project and scene "SampleScene"
2. Select "GameObject (all modified)" from the Hierarchy Window to view it in the Inspector
3. Observe the Material and Sorting Layer fields in Inspector

Expected result: blue prefab override indicators are present on the left. Right-clicking on these fields and pressing "Revert" works
Actual result: blue lines indicating Prefab Instance overrides for these fields are missing, cannot revert these fields by right-clicking and pressing "Revert"

Reproducible with: 2018.3.5f1, 2019.1.0b2, 2019.2.0a4
Not reproducible with: 2018.3.0a5 and older (no prefab overrides)

Note: the selected GameObject had all of its fields modified, however, only the Material and Sorting Layer fields do not show the overrides. Overriding and reverting the entire Prefab from the GameObject instance still works.