you broke the rules
When Alex is shot Ben says that Charles “broke the rules”. And then after when Ben is being judged by the smoke monster it’s because he “broke the rules” by allowing Alex to be killed.
What are the rules?
could it be that they are not allowed to kill children? It would kind of make sense b/c they seem like they cherish the lives of all the children, and were desperately trying to find a cure for the women so they could have more children, and they took care of the Lostie kids. It would also explain why young Ben was saved by the island after being shot by Sayid.