Here is a sample of my schema:

client.yml

Client: 
  tableName: client
  className: Client
  columns: 
    id: 
      notnull: true
      primary: true
      autoincrement: true
      type: integer
      length: 11
  relations:
    Client:
      refClass: ClientAffiliateGroup
      local: client_id
      foreign: affiliate_id
      foreignAlias: Affiliates
      equal: true

client_affiliate_group.yml

ClientAffiliateGroup:
  tableName: client_affiliate_group
  className: ClientAffiliateGroup
  columns: 
    client_id: 
      default: 
      notnull: true
      primary: true
      type: integer
      length: 11
      name: client_id
    affiliate_id: 
      default: 
      notnull: true
      primary: true
      type: integer
      length: 11
      name: affiliate_id

However, when my BaseClient?.php is generated, the setUp() looks like this:

public function setUp()
{
  $this->hasMany('Client', array('refClass' => 'ClientAffiliateGroup',
                                 'local' => 'client_id',
                                 'foreign' => 'affiliate_id',
                                 'equal' => true));

  $this->hasMany('Client as Affiliates', array('refClass' => 'ClientAffiliateGroup',
                                               'local' => 'affiliate_id',
                                               'foreign' => 'client_id'));
}

This could be user error. However, it's duplicating the Client entry, which is causing an issue because when you try to get Client->Affiliates, it brings back the wrong results because its treating affiliate_id as the local id.