My server uses a weird certificate

I created a Letsencrypt certificate and checked my site on https://www.ssllabs.com.

Certificate #1 looks ok, Certificate #2 however is not trusted. It uses a certificate from /etc/cups/ssl/server.crt which came with the OS. I am not sure why this is used with my Apache configuration.

This is how the encryption part looks like in the config currently:

SSLCertificateFile /etc/letsencrypt/live/mydomain.org-0001/cert.pem
SSLCertificateKeyFile /etc/letsencrypt/live/mydomain.org-0001/privkey.pem
SSLCertificateChainFile /etc/letsencrypt/live/mydomain.org-0001/chain.pem

Does anyone have an idea where this server.crt is configured to be used and how I can tell it to use a Letsencrypt certificate?

Edit:
I just saw that it says:

We’ve obtained this certificate while connecting to the TLS server without Server Name Indication (SNI) enabled. Only very old clients will get this certificate. Review the complete results in the simulations section.

I guess this doesn’t have anything to do with Nextcloud?

All these certificate issues are not directly related to Nextcloud. SNI is only required if you use SSL encryption of different domains (and individual certificates) with the same ip address.