There's some work in general about the repository. It would benefit you, Microsoft(dba Github), and anyone handling your repository to add a .gitignore file designed for Unity builds. There's a lot getting uploaded to the repository that's not necessary. I was able to play the game... so many questions about what I'm doing. Who is the professor. Is the professor bad?
MissingReferenceException: The object of type 'GameObject' has been destroyed but you are still trying to access it.
Your script should either check if it is null or you should not destroy the object.
SmartManager.Update () (at Assets/Scripts/SmartManager.cs:179)
From what I gather, the characters running around are put into the GameObject array 'allSmart', however when I've killed(?) one of the characters that character has been destroyed, but is still present in the array. Unity wants to access the gameobject that's been destroyed, but, alas, it is destroyed.
You'll either want to instantiate a new array each time a character is destroyed or use a List to track all the gameobjects in your SmartManager and remove the object when destroyed.
All unsolicited advice, I realize. The 'game' was the puzzle of the unbuilt entry for me.