This question is an exact duplicate of:
With the new close reasons, there is of course the option to close a question with the "custom off topic" reason. When you fill in the box, what you typed as the OT reason gets left as a comment. It seems this gets done right after the "Closed Without Comment" flag is auto-generated, though, because when I do this I immediately get a flag popup on the question telling me I haven't left a comment explaining the closure. Of course I have; the custom OT box posted my comment. But the flag is generated anyway, so I have to dismiss it.
This isn't a huge bug; it takes me all of a second to dismiss the flag. (Should I tell Community♦ it's being unhelpful, since the flag was incorrect? ;)). But on larger sites where questions might be closed by users more often, I think these invalid flags might pile up in the queue and end up wasting a good amount of a moderator's time. So I thought this was something that The Powers That Be should be aware of :)