A friend found out there is what we can refer to as a little bug in Phalcon beforeSave() model method. Even though you override it, it still doesn't work. Let me use an example to describe this

class Car
{
    public function beforeSave()
    {
        $engine = [];

        // Create a Car first Engine
        $engine[0] = new Engine();
        $engine[0]->name = 'Toyota';

        $this->engine = $engine;
    }
}

$car = new Car;
$engine = [];
$engine[0] = new Engine();
$engine[0]->name = 'Mazda';

$car->engine = $engine;
$car->save();

As expected, this is meant to save "Toyota" as the car's engine name but alas, "Mazda" is saved. I would say this is a bug in Phalcon and below is a fix for it.

Have below in the base/parent class of the model or in the model itself.

  public function beforeSave()
  {
       return $this;
  }
  public function afterSave()
  {
       return $this;
  }
  public function save($data = null, $whiteList = null)
  {
       $this->beforeSave();
       parent::save($data, $whiteList);
       $this->afterSave();
  }

Just additional, if you would like to debug your save() function not working use call a getMessages() on the object. I mean of you have

$user = new User();
$user->save();
$user->getMessages();

This works well. I guess it solves someone's problem.