### Godot version

Master (4.2)

### System information

Windows 11 - Vulkan - Nvidia RTX 4070 - intel i5 13600KF

### Issue description

As you can see in the video when you try to add multiple scenes in to the 3D viewport (only with multiple scenes) the editor throws this error.

```
ERROR: Can't add child '@Node3D@18837' to '@SubViewport@9274', already has a parent '@SubViewport@9274'.
   at: (scene\main\node.cpp:1411)
```


Video: https://youtu.be/BVcCIigQJDw

This happens in the latest master (pulled on 2.11.2023).

### Steps to reproduce

Drag couple of the 3d mesh scenes into the 3D viewport and then select multiple scenes and drag them over and observer the error.

### Minimal reproduction project

[TestSceneDragAndDrop.zip](https://github.com/godotengine/godot/files/13253741/TestSceneDragAndDrop.zip)

transform_menu->set_flat(false);
	transform_menu->set_theme_type_variation("FlatMenuButton");
	transform_menu->set_text(TTR("Transform"));
	transform_menu->set_switch_on_hover(true);
	transform_menu->set_shortcut_context(this);
	main_menu_hbox->add_child(transform_menu);
	p = transform_menu->get_popup();
	p->add_shortcut(ED_SHORTCUT("spatial_editor/snap_to_floor", TTR("Snap Object to Floor"), Key::PAGEDOWN), MENU_SNAP_TO_FLOOR);
	p->add_shortcut(ED_SHORTCUT("spatial_editor/transform_dialog", TTR("Transform Dialog...")), MENU_TRANSFORM_DIALOG);
	p->add_separator();
	p->add_shortcut(ED_SHORTCUT("spatial_editor/configure_snap", TTR("Configure Snap...")), MENU_TRANSFORM_CONFIGURE_SNAP);
	p->connect("id_pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed));
	view_menu = memnew(MenuButton);
	view_menu->set_flat(false);
	view_menu->set_theme_type_variation("FlatMenuButton");
	/
	view_menu->set_text(TTR("View"));
	view_menu->set_switch_on_hover(true);
	view_menu->set_shortcut_context(this);
	main_menu_hbox->add_child(view_menu);
	main_menu_hbox->add_child(memnew(VSeparator));
	context_toolbar_panel = memnew(PanelContainer);
	context_toolbar_hbox = memnew(HBoxContainer);
	context_toolbar_panel->add_child(context_toolbar_hbox);
	main_flow->add_child(context_toolbar_panel);
	/
	p = view_menu->get_popup();
	p->set_hide_on_checkable_item_selection(false);
	accept = memnew(AcceptDialog);
	EditorNode::get_singleton()->get_gui_base()->add_child(accept);