Once you have identified the controllers, you can hide one of them
from dom0 - not the one to which your USB device is attached, obviously.
Try interrupting the boot and editing the command line to include:
rd.qubes.hide_pci 00:1a.00 , or whatever your controller is.
If that works as expected, then you can make the change permanent by
editing the grub config.
This will ensure that one controller is used from dom0, and the other
can be safely allocated to sys-usb and used there.