### 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)

/
	MarginContainer *toolbar_margin = memnew(MarginContainer);
	toolbar_margin->add_theme_constant_override("margin_left", 4 * EDSCALE);
	toolbar_margin->add_theme_constant_override("margin_right", 4 * EDSCALE);
	vbc->add_child(toolbar_margin);
	/
	HFlowContainer *main_flow = memnew(HFlowContainer);
	toolbar_margin->add_child(main_flow);
	/
	HBoxContainer *main_menu_hbox = memnew(HBoxContainer);
	main_flow->add_child(main_menu_hbox);
	String sct;
	tool_button[TOOL_MODE_SELECT] = memnew(Button);
	main_menu_hbox->add_child(tool_button[TOOL_MODE_SELECT]);
	tool_button[TOOL_MODE_SELECT]->set_toggle_mode(true);
	tool_button[TOOL_MODE_SELECT]->set_theme_type_variation("FlatButton");
	tool_button[TOOL_MODE_SELECT]->set_pressed(true);
	tool_button[TOOL_MODE_SELECT]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_TOOL_SELECT));
	tool_button[TOOL_MODE_SELECT]->set_shortcut(ED_SHORTCUT("spatial_editor/tool_select", TTR("Select Mode"), Key::Q));
	tool_button[TOOL_MODE_SELECT]->set_shortcut_context(this);
	tool_button[TOOL_MODE_SELECT]->set_tooltip_text(keycode_get_string((Key)KeyModifierMask::CMD_OR_CTRL) + TTR("Drag: Rotate selected node around pivot.") + "\n" + TTR("Alt+RMB: Show list of all nodes at position clicked, including locked."));
	main_menu_hbox->add_child(memnew(VSeparator));
	tool_button[TOOL_MODE_MOVE] = memnew(Button);
	main_menu_hbox->add_child(tool_button[TOOL_MODE_MOVE]);
	tool_button[TOOL_MODE_MOVE]->set_toggle_mode(true);
	tool_button[TOOL_MODE_MOVE]->set_theme_type_variation("FlatButton");
	tool_button[TOOL_MODE_MOVE]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_TOOL_MOVE));
	tool_button[TOOL_MODE_MOVE]->set_shortcut(ED_SHORTCUT("spatial_editor/tool_move", TTR("Move Mode"), Key::W));
	tool_button[TOOL_MODE_MOVE]->set_shortcut_context(this);
	tool_button[TOOL_MODE_ROTATE] = memnew(Button);