The Let’s Encrypt Container used for the issue-certificate.sh script will need to have access to this port for a few seconds, so if possible, stop the other container, run the process again and this will give you the new certificate then.
Once done, you can restart the other container on port 80, but this will only postpone your problem, because the nginx container in the Mattermost distribution also wants to listen to port 80 (but you said you already changed that, so you should be good).