In my case, I was trying to use Certbot on Debian. However, it would not answer the challenge from Let’s Encrypt. I had to manually download certbot-auto, copy it to an appropriate location, run it, and then it grabbed my certificate. I also had to change it in NGinx and also my init.d files. Then, I had to change it for the automatic updates to the certificate, not to mention, tweak some settings in NGinx.
I just noticed you are trying to use Certbot. So, I need some details so that I can come up with a solution for you. What version and flavor of Linux are you using? What version of NGinx are you using? I can help you resolve this. 