For the past few days I've been dealing with a puzzling issue in Unity: Every time I called Application.LoadLevel to change the scene in my game, this would appear in my console window:
The referenced script on this behaviour is missing!
This is despite the fact that I had no missing scripts! Based on my own logging, I determined this was happening before the next scene was loaded. I ultimately found that there was an internal issue with the prefabbed objects in the scene that was to be loaded (the ones that show in blue in the hierarchy window).
I was able to eliminate the warning by:
1. From the editor, open the scene that was to be loaded during the game.
2. Go through every prefabbed object and Revert to the original prefab state.
3. Go through every prefabbed object and change all the object properties back to the way I wanted them.
It was a bit of tedious work, but the warning stopped appearing after that. My guess is this happened because I deleted a script without detaching it from some of my prefab assets first.
I hope this helps someone out there who may be experiencing the same problem and just can't pin it down!