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Take for example this question. The top answer is pretty great, and as such it has received a lot of votes. But it is not the winning answer.
Should we flag such questions for moderator attention? If not, what else should we do?
No, you should not. There is nothing a moderator can do in this situation that you cannot, and the flag would be declined as "flags should only be used to make moderators aware of content that requires their intervention" (emphasis mine).
Leave a comment for the OP informing them that another answer has won per their set challenge guidelines.
Take no action at all. As long as the challenge was open for a reasonable amount of time, there's no need to intervene.
This would require a custom moderator flag.