To be clear this is not a bug. You're simply confusing two different behaviors.

What you're describing in your example is not call-time pass-by-reference behavior. What you point 
out in the documentation does indeed refer to the changes in call-time pass-by-reference, which did 
in fact change in PHP 5.4.0.

Call-time pass-by-reference is when you call the function with your arguments passed to the function 
by reference (and not when your function prototype requires arguments to be passed by reference). 
These are two difference behaviors.

One is "pass-by-reference" and the other is "call-time pass-by-reference". The difference is that in 
the latter the references are created at the time you invoke the function (or at the time you "call" 
on the function). The former creates the references in the function prototype making them always 
available to the caller.

The form of call-time pass-by-reference this note in the manual refers to was deprecated in PHP 5.3, 
but did not issue an E_DEPRECATED error. It was removed in PHP 5.4, but the E_WARNING error you're 
referring to is not about call-time pass-by-reference. It's the fact that your function expects a 
reference and you are passing a value. This is a result of how call_user_func_array has changed from 
allowing arguments to always be passed by reference to the callback, regardless of what the callback 
function expects -- to no longer allowing this behavior by default.

Here's an example of call-time pass-by-reference behavior:

<?php
function x($a) { // notice the function does not require a reference
    return ++$a;
}


$y = 1;

/* Notice we are passing by reference at call-time */

var_dump(x(&$y)); // int(2)
var_dump($y);     // int(2)

/* Notice the &$y -- again this is call-time pass-by-reference */
var_dump(
         call_user_func_array('x', array(&$y)), // int(3)
         $y                                     // int(3)
        );
?>

In PHP >= 5.4.0 the above code would produce a fatal error of:

"Fatal error: Call-time pass-by-reference has been removed; If you would like to pass argument by 
reference, modify the declaration of x() ..." for line 11 where we call var_dump(x(&$y)). As for 
call_user_func_array(), you would not get a fatal error or a warning, but $y will still show int(1) 
since nothing is actually referenced here.

It's the case that in your test script call_user_func_array actually failed to call your function and 
the reason why you see NULL as the return value.