How to reproduce:
1. Open attached project "New Unity Project.zip" and scene "SampleScene"
2. In Hierarchy window, select "Custom Tool Object"
3. In Scene window, enable "Component Editor Tools" (a "Tools" panel in Scene view bot-right corner should appear)
4. In the "Tools" panel select/enable the only button (this is a custom button from "TestTool" Editor script)
5. Enter Play mode
6. In Hierarchy window, deselect "Component Editor Tools" object
7. Leave Play mode
8. Observe Console window

Expected result: no errors are thrown, when "Component Editor Tools" is selected the tool is visible/clickable
Actual result: Null Reference Exception is thrown, the tool does not appear anymore (until Input System)

Reproducible with: 2019.2.7f1(0.2.0, 0.9.6), 2019.3.0b4(0.9.6), 2020.1.0a5(0.9.6)
Could not test with: 2017.4, 2018.4 due to "using UnityEditor.EditorTools;" not yet implemented

Additional notes:
The issue is not reproducible if the project does not have "Input System" package installed
Reinstalling "Input System" or deleting Library folder fixes the issue until the next time repro steps are done