Florian Müllner authored Feb 20, 2017 and Michael Catanzaro committed Mar 05, 2017

Since epiphany renamed its .desktop file, web apps no longer appear
as separate applications in GNOME, but are all grouped under the
regular epiphany application. This happens because the GApplication
ID is among the properties gnome-shell uses to match a .desktop file
to a window, and as that match now succeeds, the WM_CLASS that points
to the correct .desktop file is not used at all.
It may be nice to make web apps' .desktop files use reverse notation
as well in the future and use a matching GApplication ID, but for now
just using an ID that cannot be resolved to a .desktop file is enough
to make gnome-shell fall back to matching on the WM_CLASS again.

https://bugzilla.gnome.org/show_bug.cgi?id=778985