2011 MBP i5 Mavericks
I had the same problem. App store alerted me of the iMovie update. I updated shut down and restarted, the update was reflected in the last 30 days, and it also indicated that I needed to update iMovie, having the red indicator. I checked my applications and I had the iMovie 9.09, and the current iMovie version. I deleted Both the older version, and the newer version of iMovie, emptied the trash, closed all open programs, and then pressed the off button to shut down. Waited 30 seconds and pressed the on button, waited for everything to load then click the apple in the top left ,click on software update and the red indicator was GONE. Although I have never used the application, in my compulsive nature I just downloaded it again and no red indicators. I hope this helps my fellow Apple User having the same problem : )