I am wondering too. I am confused.
in the Existing section the plugin lists all the old WordPress core files which have been obsolete. In the All section, which in the above screenshot has 491 files, the Old Core Files plugin lists all the latest WordPress core files for your reference. Therefore you ONLY have to delete files which are listed in the Existing section.
http://www.wpprohelp.com/wordpress-plugins/delete-old-wordpress-core-files-wordpress-security-tip/
Thank you. I was also confused by this. Perhaps a future update to the plugin could change the wording to make this more clear?