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After a user upvotes a comment, the option to flag as noise/offensive/spam disappears, while the up arrow icon "sticks" permanently. This has caused minor grumbling but is generally accepted as by design and not a big problem.

I just flagged a comment as noise for the first time. Afterwards, I moused over the comment and saw that the flag icon disappeared, which is slightly different behavior, but not a problem. However, the upvote arrow was still there. I clicked on it just to see if it was active, and my upvote was recorded.

The upvote option should really be disabled after a comment is flagged, both for the reason that flagging is disabled after upvoting and for consistency.

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This is not the case. I recently flagged a comment and I do not see the upvote arrow on mouseover. Please feel free to try it with this comment. – JSONBog Jun 24 '10 at 19:54
@The, you just got both from me. – Lance Roberts Jun 24 '10 at 19:55
This must be a recent bug, because I remember clearly that both icons would disappear when I flagged a comment. – mmyers Jun 24 '10 at 20:06
While these are different questions, linking this related question which brings up that upvoting a comment overrides a comment flag. – Grace Note Jan 13 '11 at 15:01
up vote 5 down vote accepted

This is a bug.

If you flag a comment and refresh the page, the controls to upvote that comment are removed. However, if you don't refresh the page, the controls remain, and as long as you wait the 5 seconds before you're allowed to vote again, the upvote goes through.

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This appears to have been fixed sometime in the intervening years.

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