Hello ANewDay,
This is a common error that many people get when using Rsync to back up files to a remote non-root account. The 640 permissions on the /etc/apf directory prevent file listing by any user other than root on the remote system, and therefore you get 'permission denied' when trying to update its contents. Most people prefer to ignore the error for /etc/apf, but if you see it for a folder that actually contains important files that need to be backed up, you may want to take action by changing the permissions to include the owner execute bit on the folder.