I made a screen capture video of this problem. Too big to post. Can email a link if that would be helpful.
From stepping through the video, I think this is what's happening: when a clone tool stroke finishes, and the mouse button is released, the screen updates (and the title bar of the image momentarily blinks gray). If another clone tool stroke begins during this update time, the problem seems to occur.
For whatever reason, I still can't reproduce the problem here.
However, for the next release, I added a check to see if the last operation had been processed before allowing a new clone operation to start. If this fixes the problem, then I should probably do something similar for Paint and Smudge which may also have the same issue.
Windows Update had me install the Windows 10 Version 1908 Feature update this afternoon. It was trivial to reproduce before, when I did the video capture, now I can't seem to reproduce this issue.