They will do that if the username and/or email address is already taken. I’ve seen it on my own instance. There are possibly other reasons as well.
If you followed the guide to use Ansible, there should be a ‘extra_themes’ folder where you put the css file.
For example, my install is in: /srv/lemmy/feddiverse.org/volumes/lemmy-ui/extra_themes
Yep, that’s the beauty of federated instances.