### 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)

scene_state.ubo.volumetric_fog_detail_spread = 1.0 / fog_detail_spread;
			} else {
				scene_state.ubo.volumetric_fog_detail_spread = 1.0;
			}
		}
	}
	if (get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_UNSHADED) {
		scene_state.ubo.ss_effects_flags = 0;
	} else if (p_render_data->reflection_probe.is_null() && is_environment(p_render_data->environment)) {
		scene_state.ubo.ssao_ao_affect = environment_get_ssao_ao_channel_affect(p_render_data->environment);
		scene_state.ubo.ssao_light_affect = environment_get_ssao_direct_light_affect(p_render_data->environment);
		uint32_t ss_flags = 0;
		if (p_opaque_render_buffers) {
			ss_flags |= environment_get_ssao_enabled(p_render_data->environment) ? 1 : 0;
			ss_flags |= environment_get_ssil_enabled(p_render_data->environment) ? 2 : 0;
		}
		scene_state.ubo.ss_effects_flags = ss_flags;
	} else {
		scene_state.ubo.ss_effects_flags = 0;
	}
	if (p_index >= (int)scene_state.implementation_uniform_buffers.size()) {
		uint32_t from = scene_state.implementation_uniform_buffers.size();
		scene_state.implementation_uniform_buffers.resize(p_index + 1);
		for (uint32_t i = from; i < scene_state.implementation_uniform_buffers.size(); i++) {
			scene_state.implementation_uniform_buffers[i] = RD::get_singleton()->uniform_buffer_create(sizeof(SceneState::UBO));
		}
	}
	RD::get_singleton()->buffer_update(scene_state.implementation_uniform_buffers[p_index], 0, sizeof(SceneState::UBO), &scene_state.ubo, RD::BARRIER_MASK_RASTER);
}
void RenderForwardClustered::_update_instance_data_buffer(RenderListType p_render_list) {