Sometimes PHP files are only meant to be called from an HTML / XHTML form. For those files, I do not post a direct link to the file, but instead a link to the HTML file which calls the PHP program.
If you run a PHP file on its own when it's expecting input from an HTML form, the results are unpredictable. Generally, you should not provide a link to a file you don't want the user to run directly. The source code for each PHP file is still available as normal.