Unwanted / duplicated temporary css files if CSS Optimization is enabled
I think your problem is about aggregate css files. The issue you give is unrelated. Each page may need a different aggregate CSS file (even in D7, it's much better than it was in D6). It results in hundreds of CSS files as you may state.

Nothing to worry about. Unused file will be deleted automatically. I can't suggest you to use Advagg module because it is only for D6 now, but take a look to have an idea about aggregate files actually work (and how they should work).