if you are using letsencrypt-auto to do everything, it should put all the files in tehre for you ( although there has been a permissions issue for some recently). If you are working in “–manual” mode then you will be told what file to put into there.
There could be a number of reasons for the same error. The first quick check is that the acme-challenge folder has permissions 755 and, if you place any file in there ( a basic one line text file is fine) you should be able to get to it in the browser