Gnome Shell doesn't recognize Wine windows
Solution 1:
In a console, type winecfg then enter. This will open the configuration tool of wine. (I think that if you type "wine config" into gnome search bar, you might also get a "Configure wine" app, it's the same).
Under "graphics", make sure "Allow the window manager to decorate the window" and "Allow the window manager to control the window" are checked.
You have to do that for all wineprefix you use.