Weird issue, I had duplicate windows when using Google Chrome’s extension for Google Hangouts. Basically, every single message in every chat window would open a duplicate window with the same contents.
Doing a bit of research, I learned it had to do with profiles. I’d inadvertently created another profile in Chrome and ended up installing Chrome Hangouts extension under that profile, whereas I already had it installed on my former profile.
Easy fix, just go through all profiles and remove the Hangouts extension under each. Profiles are accessible from the upper left corner of the Chrome window.
Options to remove the Hangouts extension is available by right-clicking on the Hangouts icon and selecting “Remove from Chrome“.