Same kind of issue here: in Unity mode, Windows doesn't appear in the dock and is looping opening applications. As soon as I let him run, it will open dozens of instances of the same application. It affects other applications since Fusion is non stop getting the focus. There is a way to get out of it without quitting or shutting down by clicking in the Fusion menu until you get the dropdown appear then you can access the window mode where you can quit all applications instances which were opened.
By the way, I had a bug with the single window or fullscreen mode because I was not able to click and found in the forum how to resolve it by closing Fusion, manually removing Fusion from the System preferences Security & privacy > Privacy > Accessibility and add it again then restart Fusion. It resolved the click bug (so now I can use it in Single mode), but got no chance with the opening application loop bug.
