How to reproduce:
1. Open the attached "ProBuilder" project
2. Open the Scene "SampleScene"
3. Press CTRL+K to create a new Cube
4. Open The ProBuilder window (Tools->ProBuilder->ProBuilder Window)
5. Select the Face Selection in the Pro Builder (at the top of the Scene view)
6. Select one side of the cube in the Scene and press CTRL+S to save the Scene
7. Press on any other side of the cube and back on the same side of the cube you have previously selected
8. Right-click on the Scene name in the Hierarchy and select "Discard changes", then press "Ok"
9. Drag the "red" Material onto the cube

Expected results: The Material is applied to the whole GameObject
Actual results: The Material can only be applied to the previously selected face

Reproducible with: 4.4.0 (2018.4.28f1, 2019.4.13f1, 2020.1.10f1, 2020.2.0b9, 2021.1.0a3)

Notes:
- Using Pro Builder 3.0.1 and older after the steps you can't even apply the Material on the GameObject, on newer Pro Builder versions the Material is applied only on the face of the GameObject
- After all the steps pressing Ctrl+Z to undo the Material apply action the face on which the Material was applied will not be rendered anymore