It's an old post but I'll reply for the case someone is having this same problem.
I had the same issue today, in my case it was an easy fix. When formatting the usb with Rufus, it's by default making a freeDOS. This doesn't work. There's an option in lower right corner to choose ISO-image. Once you choose this you get to Search for your Kali-iso. This will make your usb a bootable.