Hummingbird new features not working

I’ve used the new features on hummingbird and they don’t seem to work. I have almost of the JS combined, but Pingdom is still reporting to “Combine External JS”. Some of the files mentioned are marked as “Combine” in the Minification settings, but I can still see them in the front-end, like:

/wp-includes/js/jquery/ui/widget.min.js