The documentation describes webstub and clistub in PharPackageTask as relative path in the phar-archive.
When building on a windows system this path is build in the windows-format with \ as directory separator. Using this phar-archive in a linux-environment fails with the message: src\cli.php not found.
In the generated stub.php (nearly) all paths have / as directory separator except the entries for webstub and clistub (or are replaced by OS-independent constant DIRECTORY_SEPARATOR).
Example:
<pharpackage basedir="./" destfile="./build/${phing.project.name}.phar" webstub="./src/web.php" clistub="src/cli.php">

Result (affected lines and correct lines from generated stub.php):
$web = 'src\web.php';
...
const START = 'src\sftp_sync.php';
...
if (!file_exists($temp . DIRECTORY_SEPARATOR . md5_file(__FILE__))) { self::_removeTmpFiles($temp, getcwd()); @mkdir($temp, 0777, true); @file_put_contents($temp . '/' . md5_file(__FILE__), '');

Edit: This affects all versions at least from 2.12.0