On Mac OS X El Capitan (MacBook Pro Mid 2014) it seems that visiting the trash bin from the GUI produces a bunch of files however visiting .Trash user$ and running ls -a only produces a single file. Why would this be the case? I'm assuming the GUI defines the trash bin to be different from the terminal? If so could someone explain these definitions to me. Thanks so much
Each volume has its own trash, identified by user, in addition to the trash in your home directory. Trash shown in the dock is the aggregation of all of them.
So, in your $HOME you'll fine a .Trash, as will each user. But, also if you have other drives mounted, in the base of each will also be a .Trashes, within which will be directories for each user, identified by UID.