### 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)

tool_button[TOOL_UNLOCK_SELECTED]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_UNLOCK_SELECTED));
	tool_button[TOOL_UNLOCK_SELECTED]->set_tooltip_text(TTR("Unlock selected node, allowing selection and movement."));
	/
	tool_button[TOOL_UNLOCK_SELECTED]->set_shortcut(ED_SHORTCUT("editor/unlock_selected_nodes", TTR("Unlock Selected Node(s)"), KeyModifierMask::CMD_OR_CTRL | KeyModifierMask::SHIFT | Key::L));
	tool_button[TOOL_GROUP_SELECTED] = memnew(Button);
	main_menu_hbox->add_child(tool_button[TOOL_GROUP_SELECTED]);
	tool_button[TOOL_GROUP_SELECTED]->set_theme_type_variation("FlatButton");
	tool_button[TOOL_GROUP_SELECTED]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_GROUP_SELECTED));
	tool_button[TOOL_GROUP_SELECTED]->set_tooltip_text(TTR("Make selected node's children not selectable."));
	/
	tool_button[TOOL_GROUP_SELECTED]->set_shortcut(ED_SHORTCUT("editor/group_selected_nodes", TTR("Group Selected Node(s)"), KeyModifierMask::CMD_OR_CTRL | Key::G));
	tool_button[TOOL_UNGROUP_SELECTED] = memnew(Button);
	main_menu_hbox->add_child(tool_button[TOOL_UNGROUP_SELECTED]);
	tool_button[TOOL_UNGROUP_SELECTED]->set_theme_type_variation("FlatButton");
	tool_button[TOOL_UNGROUP_SELECTED]->connect("pressed", callable_mp(this, &Node3DEditor::_menu_item_pressed).bind(MENU_UNGROUP_SELECTED));
	tool_button[TOOL_UNGROUP_SELECTED]->set_tooltip_text(TTR("Make selected node's children selectable."));
	/
	tool_button[TOOL_UNGROUP_SELECTED]->set_shortcut(ED_SHORTCUT("editor/ungroup_selected_nodes", TTR("Ungroup Selected Node(s)"), KeyModifierMask::CMD_OR_CTRL | KeyModifierMask::SHIFT | Key::G));
	main_menu_hbox->add_child(memnew(VSeparator));
	tool_option_button[TOOL_OPT_LOCAL_COORDS] = memnew(Button);
	main_menu_hbox->add_child(tool_option_button[TOOL_OPT_LOCAL_COORDS]);
	tool_option_button[TOOL_OPT_LOCAL_COORDS]->set_toggle_mode(true);
	tool_option_button[TOOL_OPT_LOCAL_COORDS]->set_theme_type_variation("FlatButton");
	tool_option_button[TOOL_OPT_LOCAL_COORDS]->connect("toggled", callable_mp(this, &Node3DEditor::_menu_item_toggled).bind(MENU_TOOL_LOCAL_COORDS));
	tool_option_button[TOOL_OPT_LOCAL_COORDS]->set_shortcut(ED_SHORTCUT("spatial_editor/local_coords", TTR("Use Local Space"), Key::T));
	tool_option_button[TOOL_OPT_LOCAL_COORDS]->set_shortcut_context(this);
	tool_option_button[TOOL_OPT_USE_SNAP] = memnew(Button);
	main_menu_hbox->add_child(tool_option_button[TOOL_OPT_USE_SNAP]);
	tool_option_button[TOOL_OPT_USE_SNAP]->set_toggle_mode(true);
	tool_option_button[TOOL_OPT_USE_SNAP]->set_theme_type_variation("FlatButton");