What are cloned sites in Drupal 8?
Cloned site means that you copied the database instead of installing twice from scratch.

Drupal identifies two different sites as cloned sites by checking their uuid. If the uuids match, then it will assume that the sites are cloned instances.

Faulty configuration imports can lead to broken sites which we may not be able to restore. Hence to avoid this situation as discussed on https://www.drupal.org/node/2133325 a safety mechanism was introduced. And that mechanism was having a uuid for each Drupal site. 

So if you know what you are doing and you are sure that you need to import the configurations, you can use the drush cget system.site command on source site and you can use drush cedit system.site on target website to change the uuid to that from the source.