Yeah, that's a bit confusing. Mods are only human though, and they might have had a change of mind after dealing with your flag. Also, there are three of them — it could have been two different mods dealing with the flag and the closure, and mods don't always 100% agree with each other.
There's nothing to worry about though: declined flags aren't some kind of black mark on your account. (There is a tiny bonus from having a flag accepted as "helpful" in that lots add up to a couple of badges, but that's a fairly inconsequential bonus, and a single flag declined won't make much difference in progress toward the 8080 and 500500 it takes for them.) A close flag is also a fairly small (but useful! keep it up!) thing, so this doesn't represent a significant breakdown of process or anything.
At least, you can rest confident that your judgement was on-target!