### 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)

if (reload_path) {
		navigation_query->set_start_position(origin);
		navigation_query->set_target_position(target_position);
		navigation_query->set_navigation_layers(navigation_layers);
		navigation_query->set_metadata_flags(path_metadata_flags);
		if (map_override.is_valid()) {
			navigation_query->set_map(map_override);
		} else {
			navigation_query->set_map(agent_parent->get_world_2d()->get_navigation_map());
		}
		NavigationServer2D::get_singleton()->query_path(navigation_query, navigation_result);
#ifdef DEBUG_ENABLED
		debug_path_dirty = true;
#endif 
		navigation_finished = false;
		navigation_path_index = 0;
		emit_signal(SNAME("path_changed"));
	}
	if (navigation_result->get_path().size() == 0) {
		return;
	}
	
	if (navigation_finished == false) {
		
		const Vector<Vector2> &navigation_path = navigation_result->get_path();
		const Vector<int32_t> &navigation_path_types = navigation_result->get_path_types();
		const TypedArray<RID> &navigation_path_rids = navigation_result->get_path_rids();
		const Vector<int64_t> &navigation_path_owners = navigation_result->get_path_owner_ids();
		while (origin.distance_to(navigation_path[navigation_path_index]) < path_desired_distance) {
			Dictionary details;