Ah okay, if you want to run the app in a sub directory you have to modify the .htaccess file. This is how the .htacces file should look like:
# Remove index.php
RewriteEngine on
RewriteBase /sub-dir
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule . index.php [L]