Currently while running bin/phpunit as Flex recommends the first line of output contains shebang line. This makes usage of bin/phpunit impossible with e.g. PhpStorm, since version output looks like that:

$ ./bin/phpunit --version
#!/usr/bin/env php
PHPUnit 6.5.8 by Sebastian Bergmann and contributors.

$ 

The problem arises from the fact the generated bin/phpunit which is an executable with shebang contains require for simple-phpunit which also contains shebang. This may be non-bug if usage of ./bin/phpunit is discouraged (symfony/symfony-docs#9679, but why is it still generated?)