How to reproduce:
1. Open the attached “IN-132795.zip” project
2. Open the “RefsOverridesBugScene” scene
3. In the Hierarchy tab, click on the “RefHolderPrefabInstance” GameObject
4. In the Inspector tab, in “Reference Holder” component, click on “Change Reference” button
5. Observe the “Overrides Count” field. Notice that the number increases after clicking
6. In the Hierarchy tab, right-click on the “RefHolderPrefabInstance” GameObject
7. In the context menu, select Prefab → Remove Unused Overrides
8. Observe the result

Actual result: The dialog says “No unused overrides were found”
Expected result: A dialog appears suggesting to remove unused overrides

Reproducible with: 2023.2.0a13, 6000.0.68f1, 6000.3.10f1, 6000.4.0b10, 6000.5.0a7
Not reproducible with: 2023.2.0a12

Reproducible on: macOS 15.3.2 (24D81) (M1 Max)
Not reproducible on: No other environments tested