In the current design, GnomeShell provides a way to close windows from the overview (when your windows are zoomed out and visible with a close button on the top right corner).
When clicking that close button, the compositor sends a delete request to the window. This is catched by the GTK+/Clutter application and it usually closes the window.
In wayland there is currently no way to do such a thing, leaving an apparent bug in GnomeShell when running with a wayland client.

Attached a patch to GTK+ and the xdg-surface protocol description to add a delete event in the xdg protocol so we can implement the close feature on all clients.