Specifying correct StartupWMClass could prevent duplicated icons from appearing on GNOME platform.
@@ -43,6 +43,7 @@ Terminal=false
Type=Application
Categories=Graphics;
StartupNotify=false
+StartupWMClass=flameshot
Actions=Configure;Capture;Launcher;
X-DBUS-StartupType=Unique
X-DBUS-ServiceName=org.flameshot.Flameshot