Folder cannot be deleted from the Launchpad and is not displayed in Finder
In the case where only one user has a "broken" layout, you might be able to wait until the system realizes the error and fixes it.


Reboot
Look in your user home folder for an Applications folder - check there or delete it if you don't use user applications
As a last resort, view these various methods for clearing the database and settings files the dock makes to track the icons and organization of the LaunchPad: How to remove an icon from launchpad that does not appear in the Finder?


If you can drag the ghost folder from the launch pad to the dock (either in the applications section of the dock or the folders section), then locating the folder might be easier than messing with nuking the entire database or settings file.

sqlite3 $(find /private/var/folders -name com.apple.dock.launchpad 2&gt;/dev/null)/db/db "DELETE FROM apps WHERE title='Anaconda';" &amp;&amp; killall Dock