Hi @arek,
This is not considered an invalid situation.
Hmm. This sounds like a problem with your authoritative DNS server. Can you share the domain name(s) that failed this way so I can check our logs? I suspect your server returned a SERVFAIL response instead of the TXT records.
This is the way Let's Encrypt validates DNS-01 challenges today. Boulder, the Let's Encrypt server side CA software, loops over each TXT record and considers the validation successful when one matches the expected value.
Hope this helps,