Hello,
But I assume that you remove variation manually, don’t you? Because I don’t see the mentioned variations with the sold-out status in the variations list. If your product will have variation with that status you won’t get the product in the list after filtering.
Besides it’s not related to our theme but to WooCommerce plugin. You can go to Appearance > themes > install and activate Storefront theme, after that add the Filter by attribute widget to sidebar and check. You’ll get the same results.
Regards