How to reproduce:
1. Open the user's attached "PB_SubMeshInconsistency" project
2. Open the Scene "SampleScene"
3. In the Hierarchy select the "Cube"
4. Open the ProBuilder window (Tools->ProBuilder->ProBuilder Tools)
5. In the ProBuilder toolbar select Face mode
6. Select the green (top) face
7. In the ProBuilder window press "Delete Faces"

Expected results: The green Material is removed from the Cube's Mesh Renderer's Material list
Actual results: The green Material stays in the Cube's Mesh Renderer's Material list

Reproducible with: 4.0.5 (2018.4.34f1, 2019.4.25f1, 2020.3.6f1), 5.0.3 (2019.4.25f1, 2020.3.7f1, 2021.1.6f1, 2021.2.0a16)
No reproducible with: 4.0.4 (2018.4.34f1)

Note:
- If the removed face is using the Material that's last in the list of the Mesh Renderers Materials then that Material will be applied to other faces