Trying to find the reason for the cart not working, I ended up looking through the logs to find out that $woocommerce->show_messages() was causing a fatal error.

Googled a little bit and found the following

change
$woocommerce->show_messages();
to
wc_print_notices();

Made the changes and it worked.

This problem might affect people who have custom templates with woocommerce support and woocommerce might crash on update.