I'm running into this too, in PHP 5.3.6 (Apache module / CLI) on Ubuntu 11.10.

Test case directory structure:

test/
        a/
                b.php
        iterate.php
        while.php
        foreach.php
        rewind-while.php
        iterator_to_array.php
        

iterate.php is used in all of the other scripts:    
    
<?php

header( "Content-Type: text/plain" );

$it = new RecursiveIteratorIterator(

  new RecursiveDirectoryIterator(

    __DIR__ . "/a",

    FilesystemIterator::SKIP_DOTS

  ),

  RecursiveIteratorIterator::CHILD_FIRST

);


function show_items( $items ) {

  var_dump( $items );

}


$items = array();


****************************************
Expected result from all scripts:
****************************************

array(1) {
  [0]=>
  string(5) "b.php"
}


Content of the test scripts and actual results:

****************************************
while.php
****************************************

<?php

require_once "iterate.php";

while ( $it->valid() ) {

  $items[] = $it->getFilename();

  $it->next();

}

show_items( $items );

========================================

array(2) {
  [0]=>
  string(5) "b.php"
  [1]=>
  string(5) "b.php"
}


****************************************
foreach.php
****************************************

<?php

require_once "iterate.php";

foreach ( $it as $file ) {

  $items[] = $file->getFilename();

}

show_items( $items );

========================================

array(1) {
  [0]=>
  string(5) "b.php"
}


****************************************
rewind-while.php
****************************************

<?php

require_once "iterate.php";

$it->rewind();

require_once "while.php";

========================================

array(1) {
  [0]=>
  string(5) "b.php"
}


****************************************
iterator_to_array.php
****************************************

<?php

require_once "iterate.php";

$items = array_map( function ( $item ) {

  return $item->getFilename();

}, array_values( iterator_to_array( $it ) ) );

show_items( $items );

========================================

array(1) {
  [0]=>
  string(5) "b.php"
}


As you can see, iterating with `while` and `next()` produces an unexpected 
duplicate value, whereas `foreach`, `iterator_to_array()`, and the `rewind()` 
then `while` suggested by the OP produce the expected result.

You stated you're using PHP version 5.3.3 in your bug description, but your bug 
report says 5.3.16. I can not reproduce this behavior in PHP 5.3.16, however I have 
found that it is evident in early version of 5.3, prior to 5.3.10.

Steps to reproduce:

1) Create a temporary directory somewhere and your file system and create some 
empty files in that directory for testing.

`cd /tmp`
`mkdir test`
`touch test1 & touch test2 & touch test3`

2) Run the following PHP script

<?php
$directory = "/tmp/test"; 
$it = new RecursiveIteratorIterator(new RecursiveDirectoryIterator($directory));
while ($it->valid()) { if (!$it->isDot()) var_dump($it->key()); $it->next(); }
?>

Here's the output I got in PHP 5.3.2 (order is not important here):

string(15) "/tmp/test/test3"
string(15) "/tmp/test/test3"
string(15) "/tmp/test/test1"
string(15) "/tmp/test/test2"

---------------------------------

Here's the output I got in 5.3.10 all the way to the latest 5.4

string(15) "/tmp/test/test2"
string(15) "/tmp/test/test3"
string(15) "/tmp/test/test1"

------------------------------

The only potential documentation bug here is that the changelog doesn't reflect any 
changes in the behavior of RecursiveDirectoryIterator that would indicate why this 
bug existed. I haven't been able to find any bug reports on the issue, but 
obviously it was a problem at some point. I'll see if we need to update the 
changelog about this behavior and if necessary will open a bug report for SPL.

Small script to reproduce bug:

<?php
    $arr = array('first', 'second' => array('subsecond'));
    $it = new \RecursiveIteratorIterator(new \RecursiveArrayIterator($arr));
    var_dump($it->current());
    $it->next();
    var_dump($it->current());

    $it->rewind();
    var_dump($it->current());
    $it->next();
    var_dump($it->current());
?>

results:

string 'first' (length=5)
string 'first' (length=5)
string 'first' (length=5)
string 'subsecond' (length=9)

expects:

string 'first' (length=5)
string 'subsecond' (length=9)
string 'first' (length=5)
string 'subsecond' (length=9)


PHP 5.5.5, Ubuntu.

Iterators must be rewound before being used. The documentation is in error here, even if something works without being rewound in certain PHP versions. I'll update the documentation, then mark this as closed.

The example has been updated to reflect the call to rewind. As a reminder, all iterators have been designed in a way that you need to call rewind before using.