### Godot version

v4.1.stable.official [970459615]

### System information

Godot v4.1.stable - Windows 10.0.22621 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1660 Ti (NVIDIA; 31.0.15.3598) - AMD Ryzen 7 3700X 8-Core Processor (16 Threads)

### Issue description

is_input_handled() is returning True, even though set_input_as_handled() has not been called.

Example:
`func _input_event(viewport, event, shape_idx):
	print(viewport.is_input_handled())`

Returns 'True', should return 'False'

### Steps to reproduce

1. Create a new project and add a Node2D as the root
2. Add a child Area2D node containing a CollisionShape2D and a Sprite2D
3. Either create the _input_event(viewport, event, shape_idx) or connect _on_input_event(viewport, event, shape_idx)
4. Print viewport.is_input_handled()
5. True is printed.

### Minimal reproduction project

[input_test.zip](https://github.com/godotengine/godot/files/12063748/input_test.zip)

_cleanup_mouseover_colliders(true, p_paused_only);
#ifndef _3D_DISABLED
	if (physics_object_over.is_valid()) {
		CollisionObject3D *co = Object::cast_to<CollisionObject3D>(ObjectDB::get_instance(physics_object_over));
		if (co) {
			if (!co->is_inside_tree()) {
				physics_object_over = ObjectID();
				physics_object_capture = ObjectID();
			} else if (!(p_paused_only && co->can_process())) {
				co->_mouse_exit();
				physics_object_over = ObjectID();
				physics_object_capture = ObjectID();
			}
		}
	}
#endif 
}
void Viewport::_cleanup_mouseover_colliders(bool p_clean_all_frames, bool p_paused_only, uint64_t p_frame_reference) {