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You can reproduce this yourself on the demo site:
Search Builder > Contacts > Preferred Communication Method = Phone
Returns the exact same results as
Search Builder > Contacts > Preferred Communication Method != Phone
See the screenshots:
and then:
You've found a bug. Check out Reporting a Bug, starting with step 7.
As a point of interest - variations on this bug have been reported before. For instance, CRM-6652, several years ago, which was only fixed last month with CRM-16483.
If you're looking to patch this yourself, I would definitely look to CRM-16483 as a model.
in operator gives an error Notice: Undefined index: IN in CRM_Contact_BAO_Query->preferredCommunication() (line 4007 of /srv/buildkit/build/d46/sites/all/modules/civicrm/CRM/Contact/BAO/Query.php). on the CiviCRM demo site. None of the operators work when using Preferred Communication Method. This bug is really hurting the reputation of CiviCRM within our organization.