I installed a fresh symfony3-instance via the official symfony-installer (http://symfony.com/download). After doing the first things, I commited the project to Git and clone
The ScriptHandler take the dir from the extra config key in the composer.json files names as symfony-bin-dir. So check that the composer contain the correct configuration key, as example:
composer.json
....
"extra": {
"symfony-app-dir": "app",
"symfony-bin-dir": "bin",
"symfony-var-dir": "var",
....
EDIT:
The problem was related to the cache of composer. It was solved clearing it with the command:
>php composer.phar clear-cache
Hope this helps.