I also chose the option to use sys-net also as sys-usb while fresh installing 4.1 and then failed to to create a separate sys-usb. You can fix it like this:
In dom0
$ sudo qubesctl top.enabled pillar=True
You will see sys-net-as-usbvm listed there.
Then I had to clean the “leftovers” of the failed command to create sys-usb:
$ sudo qubesctl state.highstate
And finally to get rid of sys-net-usb:
$ sudo qubesctl top.disable qvm.sys-net-as-usbvm pillar=True
Runnning sudo qubesctl state.sls qvm.sys-usb now worked as expected.
Thanks to marmarek for his comment in bug #6754.