### Godot version

v4.1.dev4.mono.official [5c2295ff5]

### System information

Godot v4.1.dev4.mono - Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1660 Ti with Max-Q Design (NVIDIA; 31.0.15.3179) - Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz (12 Threads)

### Issue description

When I open my project console gets filled with these errors.

```
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: This function in this node can only be accessed from either the main thread or a thread group. Use call_deferred() instead.
   at: (scene/main/canvas_item.cpp:120)
ERROR: Condition "skeleton->size == 0" is true. Returning: RID()
   at: skeleton_get_3d_uniform_set (./servers/rendering/renderer_rd/storage_rd/mesh_storage.h:693)
ERROR: Condition "skeleton->size == 0" is true. Returning: RID()
   at: skeleton_get_3d_uniform_set (./servers/rendering/renderer_rd/storage_rd/mesh_storage.h:693)
```
### Steps to reproduce (from fresh new project)
Steps to reproduce `ERROR: Condition "skeleton->size == 0" is true. Returning: RID()` error.
1. Create new project.
1.1 Godot version used: v4.1.beta2.mono.official [a2575cba4]).
1.2 I have this setting On: Editor -> Editor Settings -> General -> Interface -> Scene Tabs -> "Restore Scenes On Load".
2. Copy/Paste .glb model with a skeleton to the project folder.
3. Double click .glb file in the editor and click Reimport.
4. Right click .glb file and select New Inherited Scene.
5. Click ctrl+s to save that scene for example player.tscn.
6. Right click player.tscn and select Instantiate.
7. Save everything and restart Godot editor. When launching editor you will see message `ERROR: Condition "skeleton->size == 0" is true. Returning: RID()` in console and Output.

### Steps to reproduce (from MRP)

Open project

### Minimal reproduction project

MRP uses v4.1.beta1.mono.official [828ec2c5d], but same error still persists
[MRP.zip](https://github.com/godotengine/godot/files/11703993/MRP.zip)

if (p_sh9) {
		if (lightmap_sh == nullptr) {
			lightmap_sh = RenderForwardClustered::get_singleton()->geometry_instance_lightmap_sh.alloc();
		}
		memcpy(lightmap_sh->sh, p_sh9, sizeof(Color) * 9);
	} else {
		if (lightmap_sh != nullptr) {
			RenderForwardClustered::get_singleton()->geometry_instance_lightmap_sh.free(lightmap_sh);
			lightmap_sh = nullptr;
		}
	}
	_mark_dirty();
}
void RenderForwardClustered::geometry_instance_free(RenderGeometryInstance *p_geometry_instance) {
	GeometryInstanceForwardClustered *ginstance = static_cast<GeometryInstanceForwardClustered *>(p_geometry_instance);
	ERR_FAIL_COND(!ginstance);
	if (ginstance->lightmap_sh != nullptr) {
		geometry_instance_lightmap_sh.free(ginstance->lightmap_sh);
	}
	GeometryInstanceSurfaceDataCache *surf = ginstance->surface_caches;
	while (surf) {
		GeometryInstanceSurfaceDataCache *next = surf->next;
		geometry_instance_surface_alloc.free(surf);
		surf = next;
	}
	memdelete(ginstance->data);
	geometry_instance_alloc.free(ginstance);
}
uint32_t RenderForwardClustered::geometry_instance_get_pair_mask() {