I noticed that on https://letsencrypt.org/howitworks/
Under “How to use the Client” I read:
The this will obtain a single cert for example.com, www.example.com, thing.is, and m.thing.is; it will place files below /var/www/example to prove control of the first two domains, and under /var/www/thing for the second pair.
I think that should read:
This will …
Probably a very quick fix