A little more detail would have been helpful. Which console do you have, presumably a new one? What image have you installed or the miscroSD card, is it the latest version of RetroPie?
The new Picade X HAT emulates a keyboard, so that’s what Emulation Station thinks it is when you start the Controller config wizard. If the arcade buttons aren’t doing what they should do, you may have have assigned them badly in the wizard. Check the last post in this thread for details on the button assignments:
If you’re still having problems, please reply with as much detail as possible.