I cannot reproduce the issue. Can you run the command with -vvv to check if there is more information then?

in ubuntu 16.04 i also cannot reproduce the issue.

@ThePooN What is the output of locale from the terminal? What distribution are you running?

hi guys,
I installed a archlinux VM with PHP and managed to recreate the issue, here is the output

Loading config file ./composer.json
Failed to initialize global composer: Composer could not find the config file: /home/osboxes/.config/composer/composer.json
To initialize a project, please create a composer.json file as described in the https://getcomposer.org/ "Getting Started" section
Reading /home/osboxes/29510/Université/symfony3/vendor/composer/installed.json

[RuntimeException]
An error occurred when generating the bootstrap file.

Exception trace:
() at /home/osboxes/29510/Université/symfony3/vendor/sensio/distribution-bundle/Composer/ScriptHandler.php:312
Sensio\Bundle\DistributionBundle\Composer\ScriptHandler::executeBuildBootstrap() at /home/osboxes/29510/Université/symfony3/vendor/sensio/distribution-bundle/Composer/ScriptHandler.php:87
Sensio\Bundle\DistributionBundle\Composer\ScriptHandler::buildBootstrap() at phar:///usr/bin/composer/src/Composer/EventDispatcher/EventDispatcher.php:297
Composer\EventDispatcher\EventDispatcher->executeEventPhpScript() at phar:///usr/bin/composer/src/Composer/EventDispatcher/EventDispatcher.php:219
Composer\EventDispatcher\EventDispatcher->doDispatch() at phar:///usr/bin/composer/src/Composer/EventDispatcher/EventDispatcher.php:81
Composer\EventDispatcher\EventDispatcher->dispatch() at phar:///usr/bin/composer/src/Composer/EventDispatcher/EventDispatcher.php:199
Composer\EventDispatcher\EventDispatcher->doDispatch() at phar:///usr/bin/composer/src/Composer/EventDispatcher/EventDispatcher.php:96
Composer\EventDispatcher\EventDispatcher->dispatchScript() at phar:///usr/bin/composer/src/Composer/Installer.php:324
Composer\Installer->run() at phar:///usr/bin/composer/src/Composer/Command/CreateProjectCommand.php:192
Composer\Command\CreateProjectCommand->installProject() at phar:///usr/bin/composer/src/Composer/Command/CreateProjectCommand.php:144
Composer\Command\CreateProjectCommand->execute() at phar:///usr/bin/composer/vendor/symfony/console/Command/Command.php:245
Symfony\Component\Console\Command\Command->run() at phar:///usr/bin/composer/vendor/symfony/console/Application.php:835
Symfony\Component\Console\Application->doRunCommand() at phar:///usr/bin/composer/vendor/symfony/console/Application.php:185
Symfony\Component\Console\Application->doRun() at phar:///usr/bin/composer/src/Composer/Console/Application.php:258
Composer\Console\Application->doRun() at phar:///usr/bin/composer/vendor/symfony/console/Application.php:117
Symfony\Component\Console\Application->run() at phar:///usr/bin/composer/src/Composer/Console/Application.php:104
Composer\Console\Application->run() at phar:///usr/bin/composer/bin/composer:56
require() at /usr/bin/composer:24

@webignition, here is the output I have for locale

LANG=fr_FR.UTF-8
LC_CTYPE="fr_FR.UTF-8"
LC_NUMERIC="fr_FR.UTF-8"
LC_TIME="fr_FR.UTF-8"
LC_COLLATE="fr_FR.UTF-8"
LC_MONETARY="fr_FR.UTF-8"
LC_MESSAGES="fr_FR.UTF-8"
LC_PAPER="fr_FR.UTF-8"
LC_NAME="fr_FR.UTF-8"
LC_ADDRESS="fr_FR.UTF-8"
LC_TELEPHONE="fr_FR.UTF-8"
LC_MEASUREMENT="fr_FR.UTF-8"
LC_IDENTIFICATION="fr_FR.UTF-8"
LC_ALL=

@ThePooN Can you confirm you have the same ?

According to my findings, the issue is with the escapeshellarg function that is escaping non ASCII characters maybe because the locale is not taken into account.
here is the line where it's happening (301)
$cmd = escapeshellarg(__DIR__.'/../Resources/bin/build_bootstrap.php');

Should be fixed by 2nd commit of symfony/flex#439

Closing as this is not a symfony/symfony issue. Thanks for reporting.