### 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)

p_render_data->scene_data->calculate_motion_vectors = true;
	} else if (!is_reflection_probe && rb->get_use_taa()) {
		p_render_data->scene_data->calculate_motion_vectors = true;
	} else {
		p_render_data->scene_data->calculate_motion_vectors = false;
	}
	
	p_render_data->scene_data->directional_light_count = 0;
	p_render_data->scene_data->opaque_prepass_threshold = 0.99f;
	Size2i screen_size;
	RID color_framebuffer;
	RID color_only_framebuffer;
	RID depth_framebuffer;
	PassMode depth_pass_mode = PASS_MODE_DEPTH;
	uint32_t color_pass_flags = 0;
	Vector<Color> depth_pass_clear;
	bool using_separate_specular = false;
	bool using_ssr = false;
	bool using_sdfgi = false;
	bool using_voxelgi = false;
	bool reverse_cull = p_render_data->scene_data->cam_transform.basis.determinant() < 0;
	bool using_ssil = !is_reflection_probe && p_render_data->environment.is_valid() && environment_get_ssil_enabled(p_render_data->environment);
	if (is_reflection_probe) {
		uint32_t resolution = light_storage->reflection_probe_instance_get_resolution(p_render_data->reflection_probe);
		screen_size.x = resolution;
		screen_size.y = resolution;
		color_framebuffer = light_storage->reflection_probe_instance_get_framebuffer(p_render_data->reflection_probe, p_render_data->reflection_probe_pass);
		color_only_framebuffer = color_framebuffer;
		depth_framebuffer = light_storage->reflection_probe_instance_get_depth_framebuffer(p_render_data->reflection_probe, p_render_data->reflection_probe_pass);
		if (light_storage->reflection_probe_is_interior(light_storage->reflection_probe_instance_get_probe(p_render_data->reflection_probe))) {