I hope it's ok to crosspost this from 2010 forums as it seems that this is also an issue in SP 2013. It's about this error when trying to delete a site column although all references have been removed from content types and lists: "Site columns which are included in content types cannot be deleted. Remove all references to this site column prior to deleting it"
Here is the "unsolved" thread from SP2010 forums:
https://social.technet.microsoft.com/Forums/office/en-US/e930964f-5c2c-4f85-bdc6-300c3a49093e/cannot-delete-site-columns-even-after-removing-all-references?forum=sharepointadminprevious&prof=required
kind regards and appreciating any help