The same error message can also be seen in the weston check serverlogs.

I think Jason Ekstrand's patch on the list might resolve this one: "[PATCH] Allow null surface arguments in wl_pointer.leave and wl_keyboard.leave"

Would be worth checking.

(In reply to comment #2)
> I think Jason Ekstrand's patch on the list might resolve this one: "[PATCH]
> Allow null surface arguments in wl_pointer.leave and wl_keyboard.leave"
> 
> Would be worth checking.

Confirmed. Jason's patch (http://lists.freedesktop.org/archives/wayland-devel/2013-June/009920.html) fixes this.

commit 9dadfb53526bc97d62dc01c165e8b6f722f7ea5a
Author: Kristian Høgsberg <krh@bitplanet.net>
Date:   Mon Jul 8 13:49:36 2013 -0400

    compositor: Eliminate marshalling warning for leave events
    
    Don't NULL the resource pointer before calling weston_surface_destroy().
    We use to have more of a distinction between compositor created surfaces
    and client surfaces, and weston_surface_destroy couldn't be used for
    client surfaces.  Now it all goes through weston_surface_destroy() and
    we can remove the assert and the NULL-ing of resource, which caused the
    marshalling warning.

diff --git a/src/compositor.c b/src/compositor.c
index a02da8b..92d89a7 100644
--- a/src/compositor.c
+++ b/src/compositor.c
@@ -1002,9 +1002,6 @@ struct weston_frame_callback {
 WL_EXPORT void
 weston_surface_destroy(struct weston_surface *surface)
 {
-       /* Not a valid way to destroy a client surface */
-       assert(surface->resource == NULL);
-
        wl_signal_emit(&surface->destroy_signal, &surface->resource);
 
        struct weston_compositor *compositor = surface->compositor;
@@ -1053,7 +1050,6 @@ destroy_surface(struct wl_resource *resource)
 {
        struct weston_surface *surface = wl_resource_get_user_data(resource);
 
-       surface->resource = NULL;
        weston_surface_destroy(surface);
 }

This issue was just reintroduced with:

commit 0d379744d34e616fea840272deda6b7027f79f55
Author: Giulio Camuffo <giuliocamuffo@gmail.com>
Date:   Fri Nov 15 22:06:15 2013 +0100

    compositor: set weston_surface:resource to NULL when destroyed
    
    with the previous patch the resource isn't used inside weston_surface_destroy()
    anymore (aside sending events unuseful for a closing client), so we can safely
    reset it.
    
    Reviewed-by: Jason Ekstrand <jason@jlekstrand.net>
    Reviewed-by: Bryce Harrington <b.harrington@samsung.com>

*** Bug 72250 has been marked as a duplicate of this bug. ***

basically 0d379744d34e616fea840272deda6b7027f79f55 reverted the fix 9dadfb53526bc97d62dc01c165e8b6f722f7ea5a

This issue breaks EFL-Wayland (https://phab.enlightenment.org/T601).  EFL-Wayland destroys it's underlying wl_surface when hiding or withdrawing windows and this issue causes Weston to disconnect the associated EFL client.  In turn the EFL main loop exits prematurely.

Fixed again in:

commit 65a07f8aef9538602792b33cb33fe856708173c0
Author: Giulio Camuffo <giuliocamuffo@gmail.com>
Date:   Fri Dec 6 12:46:27 2013 +0100

    input: make sure the devices get the resource destruction signal
    
    The device may not have a resource for the client yet, but install
    the listeners nevertheless.
    Fixes https://bugs.freedesktop.org/show_bug.cgi?id=65726