Hello,
As fro the “Clear filter does not work” Please deactivate all the plugins not related to the theme and switch the parent theme, check the issue, if the problem remains, leave the plugins not activated and provide the site admin access to the private area.
As for the products filtered from the other categories, it is the way the Woocommerce works. If the color attribute has been added to a several categories it will be shown from the several categories. You should use the WOODMART WooCommerce Layered Nav widget for filtering attributes. It has the option to set in which categories to be shown.
Best Regards