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.