### Godot version

v4.1.rc1.mono.official [1f9e540f1]

### System information

Godot v4.1.rc1.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 NavigationAgent3D is instantiated at runtime and added to the scene tree, invisible/impassable obstacle is added at the global origin position (0, 0, 0).

### Steps to reproduce

1. Run attached MRP
2. Click with `left mouse button` at the world origin to make agent walk
3. Click `space` on your keyboard to instantiate NavigationAgent3D
4. Click left mouse button to walk through world origin position again
5. Player gets stuck on obstacle at the world origin position

https://github.com/godotengine/godot/assets/8630984/fc9b32fb-25cb-46d6-9a98-ff299e2c0b1c



### Minimal reproduction project

[MRP.zip](https://github.com/godotengine/godot/files/11910363/MRP.zip)

} else {
		debug_path_mesh->surface_set_material(0, debug_agent_path_line_material);
	}
	if (debug_path_custom_point_size > 0.0) {
		Vector<Vector3> debug_path_points_vertex_array;
		for (int i = 0; i < navigation_path.size(); i++) {
			debug_path_points_vertex_array.push_back(navigation_path[i]);
		}
		Array debug_path_points_mesh_array;
		debug_path_points_mesh_array.resize(Mesh::ARRAY_MAX);
		debug_path_points_mesh_array[Mesh::ARRAY_VERTEX] = debug_path_points_vertex_array;
		debug_path_mesh->add_surface_from_arrays(Mesh::PRIMITIVE_POINTS, debug_path_points_mesh_array);
		Ref<StandardMaterial3D> debug_agent_path_point_material = NavigationServer3D::get_singleton()->get_debug_navigation_agent_path_point_material();
		if (debug_use_custom) {
			if (!debug_agent_path_point_custom_material.is_valid()) {
				debug_agent_path_point_custom_material = debug_agent_path_point_material->duplicate();
			}
			debug_agent_path_point_custom_material->set_albedo(debug_path_custom_color);
			debug_agent_path_point_custom_material->set_point_size(debug_path_custom_point_size);
			debug_path_mesh->surface_set_material(1, debug_agent_path_point_custom_material);
		} else {
			debug_path_mesh->surface_set_material(1, debug_agent_path_point_material);
		}
	}
	RS::get_singleton()->instance_set_base(debug_path_instance, debug_path_mesh->get_rid());
	RS::get_singleton()->instance_set_scenario(debug_path_instance, agent_parent->get_world_3d()->get_scenario());
	RS::get_singleton()->instance_set_visible(debug_path_instance, agent_parent->is_visible_in_tree());
}
#endif