### Godot version

v4.0.beta12.mono.official [3c9bf4bc2]

### System information

Windows 10

### Issue description

When using GetTree().ChangeScene (or GetTree().ReloadCurrentScene), the orphan node count in Monitors goes up by the number of nodes in the target scene.

This effect is amplified when running a scene that has lots of nodes.


I've also tested this in the previous beta (v4.0.beta11.mono.official [91713ced8]) and confirmed the issue didn't exist there.

### Steps to reproduce

1. Run the included Minimal Reproduction Project.
2. Open the Debugger/Monitors tab.
3. Press "Space" to load Scene2.tcsn (2 Nodes).
 - Orphan nodes increases by 2.
5. Press "Space" to load Scene1.tcsn (3 Nodes).
 - Orphan nodes increases by 3.

### Minimal reproduction project

[MRP.zip](https://github.com/godotengine/godot/files/10415860/MRP.zip)

if (call_lock && call_skip.has(n)) {
			continue;
		}
		if (!n->can_process()) {
			continue;
		}
		switch (p_call_type) {
			case CALL_INPUT_TYPE_INPUT:
				n->_call_input(p_input);
				break;
			case CALL_INPUT_TYPE_SHORTCUT_INPUT: {
				const Control *c = Object::cast_to<Control>(n);
				if (c) {
					
					
					if (c->get_shortcut_context() == nullptr) {
						no_context_node_ids.append(n->get_instance_id());
						continue;
					}
					if (!c->is_focus_owner_in_shortcut_context()) {
						continue;
					}
				}
				n->_call_shortcut_input(p_input);
				break;
			}
			case CALL_INPUT_TYPE_UNHANDLED_INPUT:
				n->_call_unhandled_input(p_input);
				break;
			case CALL_INPUT_TYPE_UNHANDLED_KEY_INPUT: