Some doubts regarding Codeigniter and its Input handling capabilities. Some may be a little weird but they are doubts none-the-less.
Whenver you use User Generated Input then pass it through the input library where it filters for xss and sql injections.
$this->input->post()
http://codeigniter.com/user_guide/libraries/input.html
Do check for more info on security filtering.
Within the CI framework check the file
Codeigniter->System-libraries->input.php
file where you can find internally the functions used by CI for sanitizing data.
XSS clean basically means filtering Out unwanted XHTML/HTML Tags