How do these sites know what framework I'm using and how do I hide it?

Honestly, when I put in my own website I'm surprised about one or two things that come up, but there's no sign of CodeIgniter in that listing. Most of the other things they list are advertised in one way or another by the server itself, and most of the client-side items can't be hidden, anyway.

The items CroNiX mentions are certainly possibilities, but if that's the case, you should probably prevent outside users from reading those files.

It's also possible that they're checking for some of the defaults configured by the framework.

Since I don't know the details of how they're figuring it out, the only thing I can really recommend is to make sure you're not serving up files on your site other than those which need to be public for your site to function, and maybe change the name of your default controller, and check some other settings, like sess_cookie_name and csrf_cookie_name. I'm guessing that a cookie named 'ci_session' is a big indicator for sites like that, since CodeIgniter is otherwise pretty good about not advertising itself.

Bonfire

Practical CodeIgniter 3
CodeIgniter Testing Guide