To reproduce:
1. Open my attached project "VerttexColorMove"
2. Open ProBuilder and Vertex Color Editor
3. Select any of the cubes in Hierarchy window
4. In Scene view, keep moving the mouse around selected object (hovering over it), while pressing ctrl+d, or ctrl+v once(if already copied the shape)
5. Try painting over the original or the newly copied object

Expected: vertex painting only affects the object which is being painted on
Actual: vertex painting affect both (or multiple) linked object (check video attached)

Reproduced in: 2018.1.2f1, 2018.2.0b6

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Vertex color painter is deprecated as of ProBuilder 4.0.0. Please use Polybrush.