To remove a document based on its ID, you need to ensure that you pass the ID as a MongoID object rather than just a string:
<?php
$id = '4b3f272c8ead0eb19d000000';
// will not work:
$collection->remove(array('_id' => $id), true);
// will work:
$collection->remove(array('_id' => new MongoId($id)), true);
?>