Many to Many Relation save process tries to update existing record nodes

Hello,

I have these objects model in my app:

Users Model:

namespace Application\Model;

class Users extends Entity
{
    public $id;
    public $firstName;
    public $lastName;
    public $gender;

    public function initialize()
    {
        parent::initialize();

        /* Created course by user (Course owner) */
        $this->hasMany('id', 'Application\Model\Courses', 'createdBy', array(
            'alias' => 'createdCourses',
            'foreignKey' => array(
                'message' => 'User cannot be deleted because he/she is courses owner in the system'
            )
        ));

        /* Teaching course by user */
        $this->hasManyToMany(
            'id',
            'Application\Model\Instructors',
            'userId', 'courseId',
            'Application\Model\Courses',
            'id',
            array(
                'alias' => 'teachingCourses',
                'foreignKey' => array(
                    'message' => 'User cannot be deleted because he/she has teaching courses in the system'
            )
        ));
    }
}

Courses Model:

namespace Application\Model;

class Courses extends Entity
{

    public $id;
    public $title;
    public $createdBy;

    public function initialize()
    {
        parent::initialize();

        /* Course creator (Owner) */
        $this->belongsTo('id', 'Application\Model\Users', 'createdBy', array(
            'alias' => 'creator'
        ));

        /* Course Instructors (Teachers) */
        $this->hasManyToMany(
            'id',
            'Application\Model\Instructors',
            'courseId', 'userId',
            'Application\Model\Users',
            'id',
            array(
                'alias' => 'instructors'
            )
        );
    }
}

Instructors Model:

namespace Application\Model;

class Instructors extends Base
{
    /**
     *
     * @var integer
     */
    public $id;

    /**
     *
     * @var integer
     */
    public $userId;

    /**
     *
     * @var integer
     */
    public $courseId;

    public function initialize()
    {
        parent::initialize();

        $this->belongsTo("userId", 'Application\Model\Users', "id");
        $this->belongsTo("courseId", 'Application\Model\Courses', "id");
    }
} 

In my controller I have create a course then select an existing user from database and assing as course instructor via magic method:

$course = new \Application\Model\Courses();
$course->title = "Sample Title";
.
.
$user = Application\Model\User::findFirst(1);
$course->createdBy = $user->id;
$course->instructors = [$user];
$course->save();

But while saving process, it tries to update that existing user to! Can someone explain what is wrong here.

Thanks.