Some of my site's pages are retrieving the .css files from a different directory
May I know where you have added CSS? on theme.info file or template.php

This issue occurring because of your theme has contained an absolute path, You need to replace absolute path the relative path.

First, you need to check that, On which file this CSS has called.

Remove from there and add CSS on theme.info file or template.php file.

On theme.info you need to add like stylesheets[all][] = custom/mytheme/css/main.css

On template.php you need to add css using drupal_add_css on template_preprocess_html(&amp;$variables).