The NginX process writes it's version output to stderr, but if it's wrapped in a script - like interacting with the Docker container like this:

# cat /usr/sbin/nginx
#!/bin/bash

/usr/bin/docker exec -it nginx $0 $@

then all the stuff goes to stdout, and a locally installed certbot is issuing an error

 The error was: PluginError('Unable to find Nginx version')

so this tiny patch fixes things up and expands the integration ability of Certbot out of the box