### 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)

main_menu_hbox->add_child(tool_button[TOOL_MODE_ROTATE]);
	tool_button[TOOL_MODE_ROTATE]->set_toggle_mode(true);
	tool_button[TOOL_MODE_ROTATE]->set_theme_type_variation("FlatButton");
	tool_button[TOOL_MODE_ROTATE]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_TOOL_ROTATE));
	tool_button[TOOL_MODE_ROTATE]->set_shortcut(ED_SHORTCUT("spatial_editor/tool_rotate", TTR("Rotate Mode"), Key::E));
	tool_button[TOOL_MODE_ROTATE]->set_shortcut_context(this);
	tool_button[TOOL_MODE_SCALE] = memnew(Button);
	main_menu_hbox->add_child(tool_button[TOOL_MODE_SCALE]);
	tool_button[TOOL_MODE_SCALE]->set_toggle_mode(true);
	tool_button[TOOL_MODE_SCALE]->set_theme_type_variation("FlatButton");
	tool_button[TOOL_MODE_SCALE]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_TOOL_SCALE));
	tool_button[TOOL_MODE_SCALE]->set_shortcut(ED_SHORTCUT("spatial_editor/tool_scale", TTR("Scale Mode"), Key::R));
	tool_button[TOOL_MODE_SCALE]->set_shortcut_context(this);
	main_menu_hbox->add_child(memnew(VSeparator));
	tool_button[TOOL_MODE_LIST_SELECT] = memnew(Button);
	main_menu_hbox->add_child(tool_button[TOOL_MODE_LIST_SELECT]);
	tool_button[TOOL_MODE_LIST_SELECT]->set_toggle_mode(true);
	tool_button[TOOL_MODE_LIST_SELECT]->set_theme_type_variation("FlatButton");
	tool_button[TOOL_MODE_LIST_SELECT]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_TOOL_LIST_SELECT));
	tool_button[TOOL_MODE_LIST_SELECT]->set_tooltip_text(TTR("Show list of selectable nodes at position clicked."));
	tool_button[TOOL_LOCK_SELECTED] = memnew(Button);
	main_menu_hbox->add_child(tool_button[TOOL_LOCK_SELECTED]);
	tool_button[TOOL_LOCK_SELECTED]->set_theme_type_variation("FlatButton");
	tool_button[TOOL_LOCK_SELECTED]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_LOCK_SELECTED));
	tool_button[TOOL_LOCK_SELECTED]->set_tooltip_text(TTR("Lock selected node, preventing selection and movement."));
	/
	tool_button[TOOL_LOCK_SELECTED]->set_shortcut(ED_SHORTCUT("editor/lock_selected_nodes", TTR("Lock Selected Node(s)"), KeyModifierMask::CMD_OR_CTRL | Key::L));
	tool_button[TOOL_UNLOCK_SELECTED] = memnew(Button);
	main_menu_hbox->add_child(tool_button[TOOL_UNLOCK_SELECTED]);
	tool_button[TOOL_UNLOCK_SELECTED]->set_theme_type_variation("FlatButton");