cakePHP: how set error validation to input field manually in controller

This can be achieved using the invalidate method that will flag the field as having an error:-

$this->Model->invalidate('field_name', 'error message');

if the $validate is defined in the model, bindModel wont cause closs of $var validate.

As for you primary question; you can set/unset/update $validationErrors of the models..eg

($remainTime < 30) {
   $this->Model->validationErrors['limitTime'] = "time is less than 30";
}