The scripting doesn't remove old messages when reuploading a file with an unallowed file type. So if I upload 2 zips while zip is not allowed then I'll see 2 messages.

This code removes duplicate messages:

          var id = $(Drupal.settings.dragNDropUploads.dropzone.wrapper + ' .form-submit[value="' + Drupal.settings.dragNDropUploads.dropzone.submit + '"]:first').attr('id');
          if (Drupal.settings.ajax[id] != undefined) {
            $('#' + Drupal.settings.ajax[id].wrapper).prev('.messages').unwrap().remove();
          }

I've added this after:

        // Upload and cleanup.
        $(dropFile).change(function() {
          $('#dragndrop-uploads').hide();
          $(origFile).replaceWith(dropFile);
          Drupal.settings.dragNDropUploads.trigger = true;