Lead Developer
You need to remove those CSS classes completely and then save the menu.
As for the IE11 issue, I just released an update (1.3.25) which fixes it. You can download it from here: https://generatepress.com/gp-1-3-25/
Documentation: http://docs.generatepress.com/
Adding CSS: http://docs.generatepress.com/article/adding-css/
Ongoing Development: https://generatepress.com/ongoing-development