I’ve seen a few different ways people have enabled (or tried to enable) certbot with Docker. My solution to this was to run a reverse proxy and certbot on the host. I wrote a guide for this type of setup if you want to have a look.
https://help.nextcloud.com/t/howto-ubuntu-docker-nextcloud-talk-collabora/76430
Can you explain what you mean by this? What are you seeing?