This error is kind of messy, I usually end up with smplayer closed and one or more icons in the system tray (smplayer indicator is set to appear in system tray), prezent but not funcţional. Sometimes the icon loses touch with smplayer (usually when there's only one instance in tray).
After restarting gnome-shell icons either dissappear (if they got no connection to any instance) or they become functional in the other case.
My system: Ubuntu Gnome 14.04.2 amd64 with kernel 3.13 (installed today on 14.04.1).
Extension: v15-1-g9dcf3fc
Shell: 3.10.4
Kernel: Linux alex-ntbk 3.13.0-46-lowlatency #79-Ubuntu SMP PREEMPT Tue Mar 10 20:23:54 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
Distribution: Ubuntu 14.04.2 LTS
Loaded Indicators: variety software-update-available indicator-cpufreq psensor y-ppa-indicator copyq smplayer
cache/upstart/gnome-session-GNOME.log :
Discarding: 14 over 15
This is SMPlayer v. 14.9.0 (svn r6778) running on Linux
Gjs-Message: JS LOG: [AppIndicatorSupport-DEBUG] registering :1.439/org/kde/statusnotifieritem/1 for the first time.
Gjs-Message: JS LOG: [AppIndicatorSupport-DEBUG] done registering
(gnome-shell:5666): GLib-GIO-CRITICAL **: g_themed_icon_constructed: assertion 'themed->names != NULL && themed->names[0] != NULL' failed
Gjs-Message: JS LOG: [AppIndicatorSupport-DEBUG] creating menu on :1.439,/org/kde/statusnotifieritem/1/menu
Gjs-Message: JS LOG: AppOutputStreamSlider
Window manager warning: Log level 8: g_variant_compare: assertion '!g_variant_is_container (a)' failed
Window manager warning: Log level 8: g_variant_compare: assertion '!g_variant_is_container (a)' failed
Window manager warning: Log level 8: g_variant_compare: assertion '!g_variant_is_container (a)' failed
(gnome-shell:5666): Clutter-WARNING **: Spurious clutter_actor_allocate called for actor 0x6f1ca40/trough which isn't a descendent of the stage!
(gnome-shell:5666): Clutter-WARNING **: Spurious clutter_actor_allocate called for actor 0x6f1ced0/vhandle which isn't a descendent of the stage!
Gjs-Message: JS LOG: [AppIndicatorSupport-DEBUG] Destroying smplayer
Gjs-Message: JS LOG: [AppIndicatorSupport-DEBUG] Destroying icon actor
(gnome-shell:5666): Clutter-WARNING **: Attempting to remove actor of type 'Gjs_AppIndicatorIconActor__1' from group of class 'StBoxLayout', but the container is not the actor's parent.
(gnome-shell:5666): Clutter-WARNING **: Spurious clutter_actor_allocate called for actor 0x6f1ca40/trough which isn't a descendent of the stage!
(gnome-shell:5666): Clutter-WARNING **: Spurious clutter_actor_allocate called for actor 0x6f1ced0/vhandle which isn't a descendent of the stage!
Gjs-Message: JS LOG: [AppIndicatorSupport-WARN] XmlLessDBusProxy::call: DBus error: Gio.DBusError: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name :1.410 was not provided by any .service files