I can't really tell what went wrong for you. I've tried both Ubuntu and Debian 9.6 boxes, and got Misago up and running in both instances. Perhaps something has been interrupted and docker just ignored it during setup? Maybe your docker installation is not up to date? Or you've deleted containers but missed volumes/configs on the retry?
I don't know how possible it would be, but maybe something didn't install right during containers creation but docker just carried on as usual. Then next setup step failed, but you've missed docker volumes and/or config directory contents? Or you've tried to salvage the situation using other means that deleting everything and trying appctl setup again with clean docker and misago_docker directories?
As for the 2 signatures not checked due to missing keys, I have also experienced this issue when installing my test instances, but both of them worked anyway.