Could be an intermittent thing where the OS doesn't yet recognize your apps icon - it can take some time for Finder (at least did in the past..)
Have you ever installed you app in the OS or at least copied the app icon to your desktop or applications folder?
From experience that triggered Finder/the OS to update its internal caches (or whatever..) and the icon started to show up properly in the dock, etc. - and probably Notification Center.
If all fails try some cache cleaner util like Onyx or logging out and back in, all of which might just trigger the OS to properly recognize your (new) apps icon.