Can ghost app updates be cleared in OS X?
In almost all cases, this is one of two things:


somewhere on your Mac, an older copy of the App is lying around and in need of an update (even though the version in /Applications is up to date)
spotlight is messed up


The first is much easier to fix, so eject all disks and network volumes and then quit and re-launch the App Store. If you still show an update, check for other copies of that app using spotlight. 

Once you are sure it's not a case of more than one app, you can go down the more complicated path of spotlight triage/repair. I like to add all drives to spotlight’s privacy pane and delete all copies of the problem app and reboot. Then turn on spotlight for just the boot volume. 

Once spotlight is done indexing that drive, go reinstall the problem app. If things are clear, enable spotlight on all remaining volumes. If not, we can cover that bigger spotlight issue in a different thread.