I have the same problem under Ubuntu 10.04.3 with PHP 5.3.5

PHP 5.3.5-1ubuntu7.2ppa1~lucid with Suhosin-Patch (cli) (built: May  7 2011 
03:15:14) 
Copyright (c) 1997-2009 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2010 Zend Technologies
    with the ionCube PHP Loader v4.0.7, Copyright (c) 2002-2011, by ionCube Ltd.
    with Suhosin v0.9.29, Copyright (c) 2007, by SektionEins GmbH

This bug is still present. The workarounds on large phar files are resulting high cpu-load and packaging phar in more than 30 mins.

Still present with PHP 5.4 as well (with Ubuntu 12.04).

PHP 5.4.12-1~quantal+1 (cli) (built: Feb 25 2013 19:19:48) 
Copyright (c) 1997-2013 The PHP Group
Zend Engine v2.4.0, Copyright (c) 1998-2013 Zend Technologies
    with Xdebug v2.2.1, Copyright (c) 2002-2012, by Derick Rethans

I also am seeing this problem in Fedora 19 Php 5.5.1. I found 2 workarounds and I'm curious if they works for others:

1. Don't attempt to compress the Phar. The compression seems to be the root of the issue and throws an exception: "unable to create temporary file"

2. Bump the number of max files that you can open by editing /etc/security/limits.conf or similar.

For whatever reason it seems that the Phar's compress method needs to open all of the files at once. Perhaps a Php Dev can shed some light on this and confirm/deny that it is a bug.

Here's a script that will trigger the bug:
(A person also narrowed down the affected C code for the phar extension: https://github.com/box-project/box2/issues/80#issuecomment-77147371 )

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

<?php

ini_set('memory_limit', -1);

$max_handles = (int) file_get_contents('/proc/sys/fs/file-max');

if (!is_dir('src')) {
    echo "Creating source files...\n";

    mkdir('src');

    $total_dirs = ceil($max_handles / 1000);

    for ($current_dir = 0; $current_dir < $total_dirs; $current_dir++) {
        mkdir("src/$current_dir");

        for ($current_file = 0; $current_file < 1000; $current_file++) {
            touch("src/$current_dir/$current_dir-$current_file.php");
        }
    }
} else {
    echo "Source files already exist, skipping.\n";
}

if (file_exists('bug.phar')) {
    echo "Removing previous phar...\n";

    unlink('bug.phar');
}

echo "Building new phar...\n";

$phar = new Phar('bug.phar');
$phar->buildFromIterator(
    new RecursiveIteratorIterator(
        new RecursiveDirectoryIterator(
            'src',
            FilesystemIterator::SKIP_DOTS
        )
    ),
    'src'
);

echo "Compression files in phar...\n";

$phar = new Phar('bug.phar');
$phar->compressFiles(Phar::GZ);

Related:

Bug #58169: "Number of files in the Phar" limited to 2042 (Apr 2008)
https://bugs.php.net/bug.php?id=58169

This is likely a duplicate of bug #70417.

I have experienced this bug in Ubuntu 18.04LTS with php 7.2.19.
I removed temp file created by Phar class, but it still fails when compressFiles is called.