What commonly happens is, for example in this question, a question is posted, somebody posts a comment linking possible dupes.
I usually post a comment mentioning why it's not a dupe, and then am linked to this meta thread: Someone flagged my question as already answered, but it's not
The top answer there suggests immediately editing your post explaining why it's not a dupe.
Why is this necessary? The only clue I get from the answer is "Not all close voters read the comments.".
It's additional information that:
If you leave that in comments, it will likely be lost. If you point out that it's not a duplicate and the person that found that dup simply deletes their comment, then that's a piece of information about your problem that is lost. And that's a problem for potential answerers and answer seekers.
Also when someone points out a duplicate, and it is "obvious" to you that it's not a dup, try and stand back a bit and have a second look at what you wrote - maybe you missed some details in your question? It's hard to write a perfectly clear question when you've been thinking about a problem for a while, you tend to be too focused and lose track of that fact that people aren't in your head and can't see all the background and your thought process.
So take that as an opportunity to clarify your question, maybe there's something that isn't quite clear when you read it from the point of view of a complete stranger.
That being said, don't just edit to say:
This question is not a dup of Fooing the bar with a frobber.
Explain succinctly why it's not a duplicate, so that people – including, perhaps, you :) – get a better understanding of the problem at hand.
(In some rare cases, someone might answer explaining that the other post does in fact solve your problem, but you're not seeing it because of some misunderstanding that they'll elaborate on. This is good too, both for you and future visitors with a related issue.)
