Files to reproduce a bug on doctrine/mongodb-odm after commit cc4960a https://github.com/doctrine/mongodb-odm/commit/cc4960a581463e6a78beb981499d5e09d1257189

OdmTestAddress.php

<?php

namespace Project\TestBundle\Document;

use Doctrine\ODM\MongoDB\Mapping\Annotations as MongoDB;

/** @MongoDB\Document(collection="odm_test_address") */
class OdmTestAddress
{
    /** @MongoDB\Id */
    protected $id;

    /** @MongoDB\String */
    protected $street;

    /**
     * Get id
     *
     * @return \MongoId $id
     */
    public function getId()
    {
        return $this->id;
    }

    /**
     * Set street
     *
     * @param string $street
     */
    public function setStreet($street)
    {
        $this->street = $street;
    }

    /**
     * Get street
     *
     * @return string $street
     */
    public function getStreet()
    {
        return $this->street;
    }
}

OdmTestUser.php

<?php

namespace Project\TestBundle\Document;

use Doctrine\Common\Collections\ArrayCollection;
use Doctrine\ODM\MongoDB\Mapping\Annotations as MongoDB;

/** @MongoDB\Document(collection="odm_test_user") */
class OdmTestUser
{
    /** @MongoDB\Id */
    protected $id;

    /** @MongoDB\String */
    protected $name;

    /** @MongoDB\ReferenceMany(targetDocument="Project\TestBundle\Document\OdmTestAddress", simple=true) */
    protected $addresses;

    public function __construct()
    {
        $this->addresses = new ArrayCollection();
    }

    /**
     * Get id
     *
     * @return \MongoId $id
     */
    public function getId()
    {
        return $this->id;
    }

    /**
     * Set name
     *
     * @param string $name
     */
    public function setName($name)
    {
        $this->name = $name;
    }

    /**
     * Get name
     *
     * @return string $name
     */
    public function getName()
    {
        return $this->name;
    }


    /**
     * Add address
     *
     * @param OdmTestAddress $address
     *
     * @return $this
     */
    public function addAddress(OdmTestAddress $address)
    {
        foreach ($this->addresses as $a) {
            if ($a->getId() == $address->getId()) {
                return $this;
            }
        }

        $this->addresses[] = $address;
        return $this;
    }

    /**
    * Remove$address
    *
     * @param OdmTestAddress $address
     *
     * @return $this
     */
    public function removeAddress(OdmTestAddress $address)
    {
        $this->addresses->removeElement($address);

        return $this;
    }

    /**
     * Get addresses
     *
     * @return ArrayCollection $addresses
     */
    public function getAddresses()
    {
        return $this->addresses;
    }
}

TestController.php

<?php

namespace Project\TestBundle\Controller;

use Symfony\Bundle\FrameworkBundle\Controller;
use Project\TestBundle\Document\OdmTestUser;
use Project\TestBundle\Document\OdmTestAddress;

class TestController extends BaseController
{
    public function testAction()
    {
        $user = new OdmTestUser();
        $user->setName('user test 1');
        
        $address1 = new OdmTestAddress();
        $address1->setStreet('street test 1');
        
        $dm = $this->get('doctrine.odm.mongodb.document_manager');
        
        $dm->persist($address1);
        
        $user->addAddress($address1);
        $dm->persist($user);
        
        $dm->flush();
    }
}