Does it help the community to flag comments that say "duplicate of question X" when it isn't an actual duplicate though the person who commented thought it was?
Should this be flagged or deleted or not?
You should not flag any comment unless it belongs to any of the followings:
If you don't agree with the comment with a duplicate link, you can make a comment using @ + commenter's user name or edit your question explaining why your question is not a duplicate. Other users with more than 3K reputation will judge based on your comment or edit.
As @pnuts explained in the comments, the possible duplicate comment is auto-generated and it doesn't necessarily mean your question is a duplicate. It will be judged by the community vote.
If you really object to it, it is not actually discouraged to flag the comment and a moderator could delete the comment if (s)he agrees with your flag. However, the link will still remain in the close-vote review queue and it will be reviewed by users. You can argue why it isn't a dupe in your comment or edit so that the flagger or close-voter may retract his/her flag or close-vote.