Drush rsync and drupal composer wrong destination dir
I had the same problem took me ages to find out what was wrong.
Turned out to be the slash (/) behind the root folder that was missing.

self.site.yml


remote:
  host: domain.com
  user: user
  root: /home/user/public_html/
  uri: http://domain.com


@see https://unix.stackexchange.com/questions/402555/why-add-a-trailing-slash-after-an-rsync-destination

Turned out to be a bug in drush
https://github.com/drush-ops/drush/pull/3405