Error when importing the configuration
This might not be the best way, but I had this same issue today. I ended up renaming language.entity.en.yml to include .OLD at the end of the filename for a backup, then I re-ran drush cim. After that it accepted my system.site.yml file. Then I took a look at the language.entity.en.yml file and for some reason it had the exact same UUID as the system.site file. I suspect the import is confused about which file is which because they both had the same UUID.