Clear Filters is not clearing the category
If you are getting annoyed at the Clear Filters button never clearing the category, you should realise that this is actually a feature of Super Speedy Filters.
To get the functionality you want, visit wp-admin > Appearance > Widgets, find your Super Speedy Show Existing Filters widget and choose Display Current Category as Removable Filter. This does two things – firstly, it adds the current category as an option to remove from the currently selected filters and secondly it updates the Clear Filters button to wipe all filters including the category – i.e. Clear Filters will now revert to the /shop/ page (or wherever the initial archive for your post type is located).