To reproduce:
1. Open attached project
2. Open scene Test. It contains a few scripts. One of them is named TestC, but in the script the class is named TesC (name mismatch)
3. Enter play mode - notice that the warning is "The referenced script on this Behaviour is missing!" and not "File and class name doesn't match"

Regression since 4.3.4f1

Explanation: If you try to add an existing MB whose class and filename don't match, you get a warning about the names not matching.
If you take an MB that has already been added to some GameObjects ("TestC") and change the class name (to "TesC"), then Unity can no longer find the MB that was referenced ("TestC")