How to reproduce:
1. Open the attached project named Case_1161994
2. Make sure the ProBuilder window is open and Vertex/Edge/Face selection modes can be selected
3. Click on any of "PB Object"'s faces, so that one face is selected
4. Select the "Plain Old Cube" object in the Hierarchy view
5. Click on a different face on "PB Object", one that was not previously selected
6. Observe that the selected face is appended to your previous selection, instead of being reset

Expected result: One face of the PB object is selected
Actual result: Multiple faces are selected as if CTRL key is pressed

Reproducible with: 2018.4.2f1, 2019.1.7f1, 2019.2.0b6, 2019.3.0a6
Could not test with: 2017.4.29f1(No package manager)

Reproducible with package versions: 4.0.2, 4.0.5
Project breaks when testing with package versions: 3.0.9 or below