### 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)

}
		RenderListParameters render_list_params(render_list[RENDER_LIST_OPAQUE].elements.ptr(), render_list[RENDER_LIST_OPAQUE].element_info.ptr(), render_list[RENDER_LIST_OPAQUE].elements.size(), reverse_cull, PASS_MODE_COLOR, color_pass_flags, rb_data.is_null(), p_render_data->directional_light_soft_shadows, rp_uniform_set, get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_WIREFRAME, Vector2(), p_render_data->scene_data->lod_distance_multiplier, p_render_data->scene_data->screen_mesh_lod_threshold, p_render_data->scene_data->view_count);
		_render_list_with_threads(&render_list_params, color_framebuffer, keep_color ? RD::INITIAL_ACTION_KEEP : RD::INITIAL_ACTION_CLEAR, will_continue_color ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, depth_pre_pass ? (continue_depth ? RD::INITIAL_ACTION_CONTINUE : RD::INITIAL_ACTION_KEEP) : RD::INITIAL_ACTION_CLEAR, will_continue_depth ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, c, 1.0, 0);
		if (will_continue_color && using_separate_specular) {
			
			RD::get_singleton()->draw_list_begin(rb_data->get_specular_only_fb(), RD::INITIAL_ACTION_CONTINUE, RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CONTINUE, RD::FINAL_ACTION_CONTINUE);
			RD::get_singleton()->draw_list_end();
		}
	}
	RD::get_singleton()->draw_command_end_label();
	if (debug_voxelgis) {
		
		bool will_continue_color = (can_continue_color || draw_sky || draw_sky_fog_only);
		bool will_continue_depth = (can_continue_depth || draw_sky || draw_sky_fog_only);
		Projection dc;
		dc.set_depth_correction(true);
		Projection cm = (dc * p_render_data->scene_data->cam_projection) * Projection(p_render_data->scene_data->cam_transform.affine_inverse());
		RD::DrawListID draw_list = RD::get_singleton()->draw_list_begin(color_only_framebuffer, RD::INITIAL_ACTION_CONTINUE, will_continue_color ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CONTINUE, will_continue_depth ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ);
		RD::get_singleton()->draw_command_begin_label("Debug VoxelGIs");
		for (int i = 0; i < (int)p_render_data->voxel_gi_instances->size(); i++) {
			gi.debug_voxel_gi((*p_render_data->voxel_gi_instances)[i], draw_list, color_only_framebuffer, cm, get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_VOXEL_GI_LIGHTING, get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_VOXEL_GI_EMISSION, 1.0);
		}
		RD::get_singleton()->draw_command_end_label();
		RD::get_singleton()->draw_list_end();
	}
	if (debug_sdfgi_probes) {
		
		bool will_continue_color = (can_continue_color || draw_sky || draw_sky_fog_only);
		bool will_continue_depth = (can_continue_depth || draw_sky || draw_sky_fog_only);
		Projection dc;