Which OS are you using? Did you do something before installing the host? It might be a problem that has been resolved in 3.2.3, which will be released soon.
Its Debian 10, installed noting before, except for (apt-get update; apt-get upgrade; apt-get update; reboot I'll fix this manually now. The LE certs are there.
Code: rm -f /usr/local/ispconfig/interface/ssl/ispserver.* ispconfig_update.sh --force seems to fix the cert problem, all services seems to use the le cert after this.