This one liner will fix your php-mcrypt, the last command tests to ensure mcrypt is properly installed.
sudo ln -sf /etc/php5/conf.d/mcrypt.ini && sudo php5enmod mcrypt && sudo service apache2 restart && php -m | grep mcrypt
Source:
https://bugs.launchpad.net/ubuntu/+source/php-mcrypt/+bug/1318021
This does solve it:
Check if mcrypt is not enabled:
root@prod:/etc/php5/mods-available# php -m | grep mcrypt
Symlinks to the wrong mcrypt.ini as a workaround:
root@prod:/etc/php5/mods-available# ln -sf /etc/php5/conf.d/mcrypt.ini .
Enabled the mcrypt mod:
root@prod:/etc/php5/mods-available# php5enmod mcrypt
Check if it was enabled:
root@prod:/etc/php5/mods-available# php -m | grep mcrypt
Restart services:
root@prod:/etc/php5/mods-available# service apache2 restart
php -m | grep mcrypt