I can confirm that this is now fixed. I updated from v3.1.6 to 3.1.7p1 and everything is working fine.
I updated from v3.1.6 to 3.1.13 and this issue is still not fixed. Also setting the permissions to /usr/local/ispconfig/interface/acme didn't do anything for me. Anyone found an actual fix for this?
So I found the reason why I was getting the error. I had to copy the file for validation in /usr/local/ispconfig/interface/acme/.well-known/acme-challenge as everything is pointed there from all domain names in ispconfig. I hope this helps someone as it took me a while to figure this out.