I get a similar issue, whereby a load of 'app was updated' notifications show all at once. Since I'm used to manually opening App Store to update, whenever the App Store automatically updates apps in the background, all the 'app was updated' notifications since the last automatic update show in the Notification Center. I do believe this is a bug, and the only way to rid of it is to either clear them off or open the App Store and force a refresh, like C DM said.