Notification Center preferences shows duplicate apps
Open terminal and run this command:
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain local -domain system -domain user && pkill Finder
Or, if you have OnyX utility app, go to "Maintenance" > "Rebuild" > check on "LaunchServices" (leave the other options unchecked) > execute