When I'm about to flag a question as, say, "off topic", I usually leave a comment to let the OP clarify the question.

Yesterday I commented this question. I asked "How is it related to worldbuilding" and got a reply:

@enkryptor you are welcome to flag it and/or make a meta about it, don't discuss it in comments.

Is it true? Why shouldn't I discuss flags in comments?

• Flags are confidential, and there's a certain risk of drama. Comments are for clarification rather than discussion, and that question's inviting discussion – Journeyman Geek Sep 2 '16 at 10:49
• @JourneymanGeek are they? "put on hold as off-topic by JDługosz, Mołot, Hohmannfan, Frostfyre, Josh King..." – enkryptor Sep 2 '16 at 10:52
• Those are close votes. Not quite the same ;p – Journeyman Geek Sep 2 '16 at 10:57

I'd say you should comment when you vote-to-close (VTC). A VTC means that the question can be improved, so the asker should know what they should improve upon. Comments should help point out the weak spots, and perhaps how to improve them.

Flagging questions usually means you want that question deleted. You probably don't need to comment for that, the mods should handle it.

I think in this case, that comment was discouraging extended discussion in comments. Which is generally discouraged. If you want to debate what is or is not on-topic on this site, meta is a better place for it.

• "that comment was discouraging extended discussion" - was it? i was hoping for the opposite. "How is it related to worldbuilding" - "I'm building a world where all bisons franticly charge to humans on sight. I want to figure out what standard measures of protection could be in this case." – enkryptor Sep 2 '16 at 13:47
• The comment "you are welcome to flag it and/or make a meta about it, don't discuss it in comments" was in response to "there is food in my world, should I post questions about cooking here?", and was suggesting you bring such questions to meta. That's what I meant, I guess I'm being overly vague. – DaaaahWhoosh Sep 2 '16 at 13:51
• I see now, yes, that makes sense. – enkryptor Sep 2 '16 at 13:53

If there is a fixable problem with a question and somebody hasn't already commented about it, leaving a comment asking for clarification or otherwise explaining the problem is a good thing. To forestall discussion in comments you can add something like "Please  to add details" (or whatever the issue was). Try to avoid conversation in comments, but please don't avoid commenting at all and surprising the user -- and anybody who was working on an answer -- with a closure later.

Another answer says that flagging means you want something deleted. That's true for many flags, but users who can't vote to close can flag to close, and close means close, not delete. (A question that stays closed could get deleted later, but the point is to hit "pause", fix the problems, and reopen.) A close flag usually sends the question to the close-votes review queue.

• Unfortunately, I find that few people actually  to add details. It's a sad state of affairs when people don't follow simple instructions from people who try to help them get their problem solved, but that's how it goes. – a CVn Apr 21 '17 at 11:51