Yes, it appears that you have hardcoded the wrong intermediate certificate in Apache.
Let's Encrypt recently changed its issuer certificate from "Let's Encrypt Authority X3" to "R3".
Usually, you will want to take the "fullchain" bundle from your ACME client (e.g. Certbot) and configure Apache's
SSLCertificateFile with that. It includes the correct intermediate certificate automatically and requires no human intervention.
What appears to have happened in your case is that you are still using the old intermediate certificate, which results in trust errors. This is usually because somebody (end-user or perhaps the developer of a buggy ACME client or integration) has hardcoded it.