This is quick note about a really obscure problem which can bite you quite hard in unity. If you switch between scene you may need to use DontDestroyOnLoad to keep certain objects hanging around during and after the transition. If, however, you have stored collections of scripts under empty game objects – and there should be an overlap between the set of scripts in a GameObject in Scene1, and Scene2, that DoNotDestroyOnLoad will prevent the GameObject containing the clashing script in Scene2 from being loaded- AT ALL! This will break things in the most unexpected and non-obvious way. For instance, RayCasters may suddenly disappear because they were never loaded (but ONLY when Scene2 is loaded via Scene1) causing User Interface elements to no longer pick up user input etc.
Bewarned.
