Large Library/Containers directory

It's likely in /Volumes/MobileBackups and you can easily delete it by entering Time Machine and navigating to the folder where the file existed. Select the file then command-click (right-click) and delete all backups of that file.

Normally, the system information window shows the backup space, but I have seen this window get hung up and not properly report storage space when Spotlight and/or the disk catalog are wonky.

You can also wipe all local backups by disabling the local store:

 sudo tmutil disablelocal

If the above steps doesn't work, you'll want to boot into recovery mode and run Disk Utility to check that the directory structure and file system catalog are correct. A fsck -fy / in single user mode is also equivalent if you are so inclined to fix things from terminal or want to perform a safe boot and have the system clean things up systematically.

The containers folder uses a Unix device called symbolic links. These links are redirects to information stored in a different folder or separate hard drive in your system. This allows for multiple paths to the same files and folders.

Some software applications can not distinguish a symlink from a valid directory and will report multiple copies of the same files and folders. There is really only one copy of the data but symlinks allow for different permissions to be applied to the application or users.

If you do a ls -la command from the terminal the first character of the permission will be the letter l (ex. lrwxr-xr-x) directories start with the letter d and files start with a dash '-' and the file name of a link will look something like this;

 lrwxr-xr-x  1 root  wheel  hidden   11B Jan 10  2014 etc -> private/etc

The first part is the file/folder name that the system is looking for and the part after the -> is the fully qualified path to the actual location of the data data. (See the man page for ls and ln for more detail.)

The function is transparent to the user from the finder but functional to the OS.

For more information do a web search on symlink or symbolic link.

P.S. While an alias that you create provides the same functionality it does it in a different way and the aliases don't backup correctly.