In that case, the flag was not handled by a moderator, but automatically by the system. (The column before "Helpful" contains the name of the moderator who handled the flag.)
I guess it is because somebody voted to close the question, and the flag was not anymore necessary, as the question appears in the review queue for the questions to close.
Generally speaking, moderators can mark a flag as useful even if there is nothing to be done, or nothing is done until later. Clearly, if a user keeps flagging as spam a post just because it contains a link, the flag is marked as wrong, to make clear to the user he is wrongly using the flag. That could be the case also when the "not an answer" flag is not used for a comment or a question that is written as answer.