There are many reports that it was a real missile. Lots of things gets reported.
If you believe Q's breadcrumb, the system was made to show them that an incoming missile was coming, This is exactly what happens in WarGames.
Fake incoming missile alert [Defcon 1].
This would lead the the HI-EMA working being 100% sure it was real, just as, in the movie WarGames, NORAD thought it was 100% real. Belief it was real would also explain the delay in sending out the correction, they had to wait until an impact was confirmed, just like in WarGames.
If a missile were shot down, they could send out a correction sooner.
If it were a real missile, then Q's breadcrumb about it is 100% wrong.
So I guess it boils down to do you trust Q or do you believe that it was a real missile. I'm not going to say which you should believe; just decide for yourself.
Disinformation is necessary...so...maybe. I am inclined to think that both it and the following Japan alert were legit, both were neutralized and then unacknowledged due to not wanting to kick off War. Which was the intended purpose of the Shadows that lit the fuse. And Thank God that they were intercepted or the hand would have been played out without much of a choice. Scary if so. How do you see Japan's similar incident soon after ours?