I'm guessing the executable permissions were removed from these files recently.
composer.json copies the following scripts (i.e., "bin": ["bin/doctrine", "bin/doctrine.php"], ) to the vendor/bin folder.
When running composer.phar update, and doctrine/orm is to be updated, composer fails because these two scripts have been chmod'd to be executable.
set permissions as expected by composer.phar update
This pull request fails (merged c1c046f into 7b75849).