### 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)

sdcache->shader = p_material->shader_data;
	sdcache->material = p_material;
	sdcache->material_uniform_set = p_material->uniform_set;
	sdcache->surface = mesh_storage->mesh_get_surface(p_mesh, p_surface);
	sdcache->primitive = mesh_storage->mesh_surface_get_primitive(sdcache->surface);
	sdcache->surface_index = p_surface;
	if (ginstance->data->dirty_dependencies) {
		RSG::utilities->base_update_dependency(p_mesh, &ginstance->data->dependency_tracker);
	}
	
	sdcache->shader_shadow = material_shadow->shader_data;
	sdcache->material_uniform_set_shadow = material_shadow->uniform_set;
	sdcache->surface_shadow = surface_shadow ? surface_shadow : sdcache->surface;
	sdcache->owner = ginstance;
	sdcache->next = ginstance->surface_caches;
	ginstance->surface_caches = sdcache;
	
	sdcache->sort.sort_key1 = 0;
	sdcache->sort.sort_key2 = 0;
	sdcache->sort.surface_index = p_surface;
	sdcache->sort.material_id_low = p_material_id & 0xFFFF;
	sdcache->sort.material_id_hi = p_material_id >> 16;
	sdcache->sort.shader_id = p_shader_id;
	sdcache->sort.geometry_id = p_mesh.get_local_index(); 
	sdcache->sort.uses_forward_gi = ginstance->can_sdfgi;
	sdcache->sort.priority = p_material->priority;
	sdcache->sort.uses_projector = ginstance->using_projectors;
	sdcache->sort.uses_softshadow = ginstance->using_softshadows;
}
void RenderForwardClustered::_geometry_instance_add_surface_with_material_chain(GeometryInstanceForwardClustered *ginstance, uint32_t p_surface, SceneShaderForwardClustered::MaterialData *p_material, RID p_mat_src, RID p_mesh) {