<?php
class Foo {
  function __construct (&$arr) {
    $this->arr = &$arr;
  }
  function createInstance () {
    $reflectionClass = new ReflectionClass("Bar");
    return $reflectionClass->newInstanceArgs(array($this, $this-
>arr));
  }
  function mod($key, $val) {
    $this->arr[$key] = $val;
  }
}

class Bar {
  function __construct (&$foo, &$arr) {
    $this->foo = &$foo;
    $this->arr = &$arr;
}
  function mod($key, $val) {
    $this->arr[$key] = $val;
  }
}

$arr = array();

$foo = new Foo($arr);

$arr["x"] = 1;

$foo->mod("y", 2);

$bar = $foo->createInstance();

$bar->mod("z", 3);

var_dump($arr,$foo,$bar);

?>

It works when the elements of the array are references:

$reflectionClass->newInstanceArgs(array(&$this, &$this->arr));

The current behavior here is correct and intended. As mentioned, you need to use references in the array to allow this to work in any reasonable fashion.

Since PHP 7.1 the call will be performed despite the reference warnings, though this may be tightened again in the future.