On beta sites, when a question is closed and there is no comment at all on it, an automatic flag is raised. The idea is that each closure should be explained, as a beta site is still defining the scope.
The part that makes this flag annoying is that it does not get dismissed automatically once a comment is posted. I have to manually dismiss it if I close first and comment later, which I usually do. Of course I could reverse the order, but there is still another case where it fails now.
If I choose to close using a custom reason, a comment gets added explaining the closure. But the automatic flag urging me to comment still gets raised.
I think the cleanest way to solve both issues would be to have any new comment on that question trigger the dismissal of the flag.