Twice loading config's files

Hello, help please

1. We traced php process which works on Code Igniter and we get data:
access("/var/www/name.com/apps_files/config/config.php", F_OK) = 0
access("/var/www/name.com/apps_files/config/production/config.php", F_OK) = -1 ENOENT (No such file or directory)

2. We fix it and created symlink /production/config.php to /config/config.php and look: is it will enought if it will find file from first time and we get next data
access("/var/www/name.com/apps_files/config/config.php", F_OK) = 0
access("/var/www/name.com/apps_files/config/production/config.php", F_OK) = 0

 Problem that core CI load twice same config file, how we can fix it? 

It was working fine before you broke it. Of course it load twice now that you created a symlink to the same file! Why did you do that? The second file is there to set configuration for a specific environment to override the global configuration.