every time you execute the php in your console.
It means that you have already activated the apc.so extension.
You must check the second module activation.
Here you can find the apc.ini config file
$ locate apc.ini
/etc/php5/conf.d/20-apc.ini
/etc/php5/mods-available/apc.ini
Now locate php.ini files and check them for uncommented "extension=apc.so" line
$ locate php.ini
/etc/php5/apache2/php.ini
/etc/php5/cgi/php.ini
/etc/php5/cli/php.ini
check files for uncommented "extension=apc.so"
$ cat /etc/php5/apache2/php.ini | grep apc.so
;extension=apc.so
Here you found it
$ cat /etc/php5/cli/php.ini | grep apc.so
extension=apc.so
Edit the file
sudo vim /etc/php5/cli/php.ini
and add ";" before "extension=apc.so"
save it and you are done
Source: http://blog.ciuly.com/my-server/php-warning-module-apc-already-loaded-in-unknown-on-line-0/