### 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 (agent_parent == nullptr) {
		return;
	}
	if (!agent_parent->is_inside_tree()) {
		return;
	}
	if (!target_position_submitted) {
		return;
	}
	update_frame_id = Engine::get_singleton()->get_physics_frames();
	Vector3 origin = agent_parent->get_global_position();
	bool reload_path = false;
	if (NavigationServer3D::get_singleton()->agent_is_map_changed(agent)) {
		reload_path = true;
	} else if (navigation_result->get_path().size() == 0) {
		reload_path = true;
	} else {
		
		if (navigation_path_index > 0) {
			const Vector<Vector3> &navigation_path = navigation_result->get_path();
			Vector3 segment[2];
			segment[0] = navigation_path[navigation_path_index - 1];
			segment[1] = navigation_path[navigation_path_index];
			segment[0].y -= path_height_offset;
			segment[1].y -= path_height_offset;
			Vector3 p = Geometry3D::get_closest_point_to_segment(origin, segment);
			if (origin.distance_to(p) >= path_max_distance) {