File Permissions on Compiled Templates
Normally folders in the /craft/storage/runtime/* directory are just cached files.

Those files are generated by craft, so really they're generated by php/php-fpm/nginx/apache or what ever you've got setup.
Maybe check the user that made those folders are in the www-data group if you do want to look into it further.

The better solution is to completely ignore that folder... Those files do not need to be deployed at all. They're just cached files generated by Craft. So just ignore that directory from your repo completely.