Steps:
1. Open attached project
2. Use "Test/Run" menu item
==>
"Error: The Prefab contents root has been deleted" dialog appears

The script is

[MenuItem("Test/Run")]
public static void Run()
{
var prefabStage = PrefabStageUtility.OpenPrefab("Assets/Cube.prefab");
var root = prefabStage.prefabContentsRoot;

Undo.DestroyObjectImmediate(root);
}

Expected behaviour is that Undo.DestroyObjectImmediate throws an exception just like Object.DestroyImmediate does