$this->form_validation->set_rules('form_field', 'form_label', 'is_unique[table.field]');

UNIQUE INDEX `id_aluno` (`id_aluno`, `ano`),

$this->form_validation->set_rules('form_field', 'form_label', 'callback_combpk[$pk2]');
    public function combpk($pk1, $pk2)
        {
               $this->db->where('field1', $pk1);
               $this->db->where('field2', $pk2);
               $result = $this->db->get('table');
               if($result->num_rows() > 0)
               {
                  $this->form_validation->set_message('combpk','something'); // set your message
                  return false;
               }
               else{ return true;}

        }

$last_id = $this->model->set();
if ($last_id === FALSE)
    if ($this->db->_error_number() == 1062)
        $this->data['message_error'] = 'Not unique.';
    else
        $this->data['message_error'] = 'Database error.';