Product and version : 126.96.36.1992
OS and version: OS X 10.11.6
Hardware: MacBook Pro (Retina, 15-inch, Mid 2015)
One file open, displaying five windows.
Three windows showed unique layouts.
Two windows showed the same layout, sized to focus on different parts of the layout. These are the windows that displayed the issue.
When moving/adjusting one window the other window moved.
How to replicate
I'm not sure of the exact conditions needed to replicate. This happened twice in slightly different situations both related to adjusting the size of one window. As the window size started to change the other window jumped to the left.