What @bruncsak described was more a different between your command prompt and the environ your auto-renew runs in. Does that run as a cronjob or a systemd timer? You didn't describe your O/S or Certbot version so I can't tell. You can review which option from these docs User Guide — Certbot 2.11.0.dev0 documentation
Sometimes the cronjob may not be using the same shell so gets a different PATH which then might see the wrong software version or config compared to something in the command line.
I found a very old but similar sounding problem below. Does any of the above or thread below sound plausible?