I stumbled upon this issue myself as well and found the solution for multilingual Prestashop in combination with the friendly URL setting.
In your nginx config you can add the following rule to handle multilingual calls to the index.php. In this case "nl" and "en", if you need more languages you can add them separated by a pipe.
location ~ (/nl|/en)/index\.php$ { try_files $uri $uri/ /index.php?$args; }