I usually close most of my apps at the end of the day by using Command+Tab followed by Command+Q. When I do this with Logos it only closes the main Logos window and will not close any of the floating windows. I usually have to force close Logos, and even then it has taken up to five minutes for my Mac to process this request.
I also found this happening when I installed an update to my Mac last week (though at the time I thought it was a fluke). My Mac asked me to restart, which I did. When the Mac began closing apps, it said that Logos stopped the restart. Again, the main window was gone, and only the floating windows remained open. I had to force quit Logos to allow my Mac to restart and install the update.