After running a Mattermost cli command one or more plugins is missing from the Plugins section of the System Console.
When running a cli command with a user other than the mattermost user the permissions of the plugins folder will get changed to be owned by the user that ran the command. To prevent this from happening you can either run the cli command as the mattermost user using:
sudo -u mattermost bin/mattermost
or by using mmctl instead.
To fix this you can simply change ownership back to the mattermost user by running:
sudo chown -R mattermost:mattermost /opt/mattermost