It appears Ubuntu 18.04 has a much newer version of gnome-shell-
extension-ubuntu-dock. Can you please try that?
http://cdimages.ubuntu.com/daily-live/current/

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https://bugs.launchpad.net/bugs/1744471

Title:
  Dock erroneously shows generic icon with org.*.desktop file

Status in gnome-shell package in Ubuntu:
  Incomplete
Status in gnome-shell-extension-ubuntu-dock package in Ubuntu:
  Incomplete

Bug description:
  Launching an application which has a desktop filename of the form
  <org.user.application.desktop>, the generic application icon appears
  in the dock.

  If the desktop filename is changed to the form <application.desktop>,
  the icon that appears in the dock is the one specified in the desktop
  file.

  Ubuntu 17.10 / Wayland
  gnome-shell-extension-ubuntu-dock 0.7.1

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