I have a red "1" on my App Store icon, as if there were an update ready to be downloaded. But every time I check for updates, the app store says there are no new updates. Why won't the red "1" go away?
Some folks appear to have a bug in the Mac App Store app.
You could try reindexing your HDD. The MAS usues the Spotlight indexing in determining what apps need updating. Go to Sys Prefs/Spotlight/Privacy, add your HDD to the list then remove it from the list. Spotlight will then reindex your HDD.