I’m not the expert but had maybe similar problem. Also, below explanation may not be accurate because I get it from my memory 
In the last version, bench doesn’t support certbot-auto anymore. So the command will fail. But the certs definition in the site_config is still created. So when doing bench setup nginx and bench setup reload-nginx will fail.
My solution: check if the path to certs are all correct:
- in the site_config.json
- nginx.conf
- if wildcard, also check in common_site_config.json
I hope this help.