Drush not working on a docker based enviroment on ubuntu 16.04
When you run docker run ... or docker-compose run, Drush is running in the context of the container, not your host machine. So when it needs stuff like DB credentials, aliases, ssh keys, it looks for them in the container. If Drush cannot find such things in the container, Drupal cannot fully connect to Drupal and you get an error, usually the bootstrapping one.

I have a feeling your code isn't mounted to the Drush container, based on the fact that the alias scanning isn't picking up anything custom, only the usual alias paths. If the code is mounted, then probably the Drush container does not have the DB credentials. Do a drush status to check if everything is fine.