When running a program in a non virtual desktop, all programs' windows are added both to the virtual desktop and to the default desktop (but not to all desktops ).

The default desktop is something like a "trash" desktop that always contains all windows (other desktops only contain their own windows). I already had some requests to change this, but I have to consider all this people who want to have a way to easily (and quickly) go back to a complete desktop when they want to do so.

If you don't want to use this desktop, exclude it from the virtual screen and never switch to it.