I don't know why but after calling the singleton:
MyModel::findById($id)
...the source collection I defined on the model constructor changes from 'myCustomCollection' to 'my_model'
I fixed it by adding some temporary code inside the _getResultSet method from app/vendor/phalcon/incubator/Library/Phalcon/Mvc/MongoCollection.php (Line 310)
$cursor->setTypeMap(['root' => get_class($base), 'document' => 'array']);
if (true === $unique) {
/**
* Looking for only the first result.
*/
$output = current($cursor->toArray());
$output->setSource($base->getSource());
return $output;
}