I am getting an error using PhpExpress on Linux.

[NuSphere PhpExpress] NuSphere PhpExpress 2.0.3 can not be loaded twice.
PHP Warning: [NuSphere PhpExpress] NuSphere PhpExpress 2.0.3 can not be loaded twice in Unkown on line 0

when running script from the command line with the shebang line #!/usr/bin/php -q

I use scripts running from the command line as well as php scripts from a webserver on the same machine. The web server is Lighttpd 1.4.2 using the FastCGI module.

I have PHP 5.2.9

I get this error even if the scripts arent encoded with Nu-coder.

Is there a way to stop this? the script runs fine after the error, but i want to clean up the errors.

Do you mean that without shebang line all works fine?
Different versions of PHP are handling shebangs differently. I'd recommend you to try the latest.