How to reproduce:
1. Create a new project with ProBuilder asset package
2. Tools/ProBuilder/ProBuilder Window
3. New Shape -> Build Door
4. Vertex Colors -> Paint a few vertices of the door
5. Undo a few times
6. Observe the errors in the console:
"Mesh.colors is out of bounds. The supplied array needs to be the same size as the Mesh.vertices array.
UnityEngine.Mesh:set_colors(Color[])
pb_VertexColor_Editor:OnSceneGUI(SceneView)
UnityEngine.GUIUtility:ProcessEvent(Int32, IntPtr)"

Reproduced with: 5.6.6f1, 2017.4.1f1, 2018.1.0f1, 2018.2.0b1, 2018.3.0a1-c6c068127f2b

Note: Not reproducible with all shapes.

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The vertex painter in ProBuilder is deprecated as of ProBuilder 4.0.0. It's functionality is superseded by Polybrush.