could you give some information on how you flashed the Ubuntu installer onto your USB device? In my experience it's quite easy to end up with something that just won't work on macs. It's also not super straight forward to create a bootable USB installer on OS X, here's a guide - https://itsfoss.com/create-bootable-ubun... - that seems to get it right, can't test it myself though as I don't own a a mac any more.
All right, I misunderstood your first post a little. Just to be sure, I would definitely try to reset NVRAM and PRAM as detailed here: https://support.apple.com/en-us/HT204063
If that doesn’t help and you are currently able to boot into Ubuntu (even if only on your HDD with some broken sectors), you could check if the the USB device shows up under the OS correctly (e.g. by executing lsblk) and even just write a fresh Ubuntu installer onto it via the dd command (there’s many guides how to do this online and you don’t need any additional tool to create a bootable USB under linux).
If neither suggestion works I’m afraid you’ll need a more knowledgeable person than I.