### 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)

{
		origin_enabled = true;
		grid_enabled = true;
		indicator_mat.instantiate();
		indicator_mat->set_shading_mode(StandardMaterial3D::SHADING_MODE_UNSHADED);
		indicator_mat->set_flag(StandardMaterial3D::FLAG_ALBEDO_FROM_VERTEX_COLOR, true);
		indicator_mat->set_flag(StandardMaterial3D::FLAG_SRGB_VERTEX_COLOR, true);
		indicator_mat->set_flag(StandardMaterial3D::FLAG_DISABLE_FOG, true);
		indicator_mat->set_transparency(StandardMaterial3D::Transparency::TRANSPARENCY_ALPHA_DEPTH_PRE_PASS);
		Vector<Color> origin_colors;
		Vector<Vector3> origin_points;
		const int count_of_elements = 3 * 6;
		origin_colors.resize(count_of_elements);
		origin_points.resize(count_of_elements);
		int x = 0;
		for (int i = 0; i < 3; i++) {
			Vector3 axis;
			axis[i] = 1;
			Color origin_color;
			switch (i) {
				case 0:
					origin_color = get_theme_color(SNAME("axis_x_color"), EditorStringName(Editor));
					break;
				case 1:
					origin_color = get_theme_color(SNAME("axis_y_color"), EditorStringName(Editor));