If you flag a comment that happens to have been deleted before you flagged it (probably because several other people have flagged it) then a red box is displayed that states that that comment no longer exists. Ordinarily flagging a comment will not display anything.
I don't think that flagging a comment that doesn't exist is so significant that I should see a big error box when it happens. This is made even worse by the fact that I can't do anything about it!
If you feel like you have to display something to me when I try to flag an offensive, spammy or abusive comment that doesn't exist anymore, then please don't make it look like I've done something wrong. Make it something that is happy and cheerful because this one little piece of offensiveness, spam or abuse is no longer a part of this world.
Edit: Since this feature is probably behaving as designed I've retagged the post as a feature-request.