If two windows show a single buffer, then the region highlighting is
strange in the non-selected window.  It is not hard to reproduce,

    1. emacs -Q
    2. Visit a longish file.
    3. C-x 3 and scroll up in any of the window.
    4. M-: (setq highlight-nonselected-windows t) RET.
    5. Create an active region and compare the highlighting.

I'm attaching a screenshot to demonstrate the issue in case the
reproducer wasn't clear.