That doesn't sound like an error from Let's Encrypt. 
A Let's Encrypt error message might have been, for example, "DNS problem: SERVFAIL looking up TXT for _acme-challenge.example.com".
The authz at https://acme-v01.api.letsencrypt.org/acme/authz/3Xh94A0Vn5JzJKkHOXneZkMJUPfwszAP5NzMyrD2xLU also reports that it's been deactivated by the client, not that there was an error and validation failed.
It sounds like the ACME client itself is making some sort of DNS query, and that's failing. Maybe the local DNS resolver is experiencing an issue?