QTFile is just javascript and therefore just UI code, the upload is handled by server side code. Really it wasn't intended to use file manager to manage css files, probably you just need to add css as an allowed upload extension in web.config/user.config so that the server side code allows uploading. There is nothing broken nor needing update in the QTFile code that I know of at this point though I have not yet looked into the issue with .html files it doesn't sound like a javascript error.
You can copy the AllowedUploadFileExtensions setting from web.config into user.config and add any extensions that you want to be able to use.
Hope that helps,
Joe