When deleting phone numbers/emails from non-constituent relationship records that were added prior to the 7.94 update, the deleted phone numbers/emails are still appearing in query results, even though they no longer exist on the relationship record. Newly added non-constituent relationships, the query will reflect the correct phone information, even after deleting a phone number/email.
Download and install the latest patch, which contains all fixes from previous patches. If you are running an older version, download and install the latest version and then the patch.
Include the query on an Export, then select the phone fields from the Output tab.