I'm using IIS8, though I think this might apply to any version of IIS from 7 or higher.
I wanted to remove a module for a specific site (DirectoryListingModule), so I opened the Modules module and removed it, only to find the Directory Browsing icon still in my module list. I can still enable it and configure it. When I try to load the website, I get an HTTP Error 500.21 - Internal Server Error caused by my web.configs. I looked around and found that my ApplicationHost.config removes the DirectoryListingModule for my site, and then my site's web.config tries to configure it, causing a conflict.
Up to there, I understand why it is causing problem. The part I do not understand is why, even though the module has been removed, can I still see it and configure it. Shouldn't it be hidden or not configurable, or at least warn me that the module is removed for this site ?