When VIVO looks for a phone number, it queries for all vcard telephoneNumbers and removes the fax and others, leaving only the ones without types, which it assumes are the phone numbers.
Phone numbers should be typed as phones (not faxes). Then a positive SPARQL query can be used to find them.
Phone number types will need to be reviewed and one or more types added.
Then all phone numbers without types should be asserted to be phone number type (this is the assumption made in the current SPARQL queries).
This requires a datastore change for VIVO sites upgrading to a version of VIVO in which this is fixed.