theslitherydeee: It should go away about an hour after you've clicked on the game in question.
To be more precise: I think you need to click on the download button for the game (or updated component), before the flag goes away. I usually click the download button (in non-downloader mode) and cancel the download right away, just to get rid of the pesky notification.
Sometimes the notification goes away right away, sometimes it stays there for hours or days. Someone mentioned Dragonsphere, for some reason it didn't even show which downloadable component was updated, and even if clicking on all of them, the notification would still stay there. But now it is finally gone.