Description:
------------
php-pecl-mongo version 1.4.5

I don't really think that it's problem in mongo pecl module, because this is problem  of an inside PHP Engine (optimizations for passing variables by reference before it's changed).

Test script:
---------------
function prepare() {
    return [
        'key' => 'test1',
        'create' => time(),
        'update' => 0,
        'value' => 0
    ];
}
function save($array2) {
    $db = (new Mongo('localhost'))->selectDB('test');
    $collection = $db->selectCollection('test');
    // array2: new field `_id` would be added, insert requesting param by reference
    $collection->insert($array2);
    // `some` field only in array1, but `_id` field in both arrays
    return $array2;
}
$array1 = prepare();
$array2 = save($array1);
// array1: add `some` field to array1
$array1['some'] = true;
var_dump(isset($array1['_id']), isset($array2['_id']), isset($array1['some']), isset($array2['some']));

Expected result:
----------------
bool(false)
bool(true)
bool(true)
bool(false)

Actual result:
--------------
bool(true)
bool(true)
bool(true)
bool(false)