The trash seems to be empty, but the partition's trash folder (.Trash-1000) shows the deleted files and they keep taking up space. Is this a bug in the new version (16.10) released today? Everything was working fine a few hours ago before upgrading to the new 16.10 edition.
As mentioned earlier (see my comment to your question), I filed a bug report which was merged with this report -> https://bugs.launchpad.net/ubuntu/+source/glib2.0/+bug/1633824. The root cause could be located - it was an issue with the glib2.0 packages and finally a fix is released.
To apply the bug fix, enable the yakkety-proposed repository as described here. Then open a terminal and execute : sudo apt install libglib2.0-0 libglib2.0-bin libglib2.0-data. Afterwards log out and back in and now everything regarding the trash will work as expected.
To revert back the configuration, disable the yakkety-proposed repository. Of course you alternatively can wait until the new glib2.0 version is released to the main repositories.
~/.local/share/Trash/if you didn't delete it by Shift+Delete – Benny Oct 13 '16 at 21:25