Yes, Both Mac OS X 10.11 and 10.12 suffer from this inability to bring windows to the front. It has nohing to do directly with Sigil. This did not happen much in 10.10. I have found no solution. Simply look at the Finder Dock and click the Python icon there to bring that Window to the front.
I have seen the same behaviour with Mail, Safari, and Excel windows opening under other apps on 10.11 and 10.12. Hopefully Apple will fix this soon.
KevinH
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