### 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)

}
					}
				}
			}
			
			emit_signal(SNAME("waypoint_reached"), details);
			
			if (waypoint_type == NavigationPathQueryResult2D::PATH_SEGMENT_TYPE_LINK) {
				emit_signal(SNAME("link_reached"), details);
			}
			
			navigation_path_index += 1;
			
			if (navigation_path_index == navigation_path.size()) {
				_check_distance_to_target();
				navigation_path_index -= 1;
				navigation_finished = true;
				target_position_submitted = false;
				if (avoidance_enabled) {
					NavigationServer2D::get_singleton()->agent_set_position(agent, agent_parent->get_global_position());
					NavigationServer2D::get_singleton()->agent_set_velocity(agent, Vector2(0.0, 0.0));
					NavigationServer2D::get_singleton()->agent_set_velocity_forced(agent, Vector2(0.0, 0.0));
				}
				emit_signal(SNAME("navigation_finished"));
				break;
			}
		}
	}
}
void NavigationAgent2D::_request_repath() {