Doctrine\ODM\MongoDB\Query\Expr::getNewObj() uses Doctrine\ODM\MongoDB\Persisters\DocumentPersister::prepareQuery() method for preparing newObj. However, prepareQuery is not suitable for that.

The first lines in prepareQuery method should apply to find queries only:

if (is_scalar($query) || $query instanceof \MongoId) {
$query = array('_id' => $query);
}
if ($this->class->hasDiscriminator() && ! isset($query[$this->class->discriminatorField['name']])) {
$discriminatorValues = $this->getClassDiscriminatorValues($this->class);
$query[$this->class->discriminatorField['name']] = array('$in' => $discriminatorValues);
}

Recommendation: DocumentPersister should introduce a new method, such as prepareNewObj($newObj) for preparing the newObj array. Expr::getNewObj() should be change to invoke the new method.