Some sites missing letsencrypt intermedaite certyficate for no reson

The intermediate cert is in the certificate file, it's not a separate file anymore in recent apache versions. Take care that you looked into the right file. And the files are created by certbot, not ISPConfig.

 

First, check if the intermediate SSL cert is included in the SSL crt file. If that's the case, then check in a real browser, not an SSL tester. Results from SSL test sites are not always correct, so don't worry if they show sites unless you get the same error in a browser.

 

I just checked your ssl cert for you, the cert of that site is valid and it also has the correct full certificate chain.

 

Click on the SSL icon in the URL bar of the browser, open the SSL details and check the cert chain.

 

Check it in your browser. Your users are using a web browser to browse your site and not an SSL tester. And if you don't believe me and your web browser, then read the apache documentation yourself to see that chain certs belong into the crt file now and then check the crt file to see if LE has added the chain cert there or not. How many customers did you have that told you that they can't browse your site due to an SSL error?