systemd-nspawn handles permissions for devices through [cgroups][1]. By default, any container is granted with permissions only for common devices like /dev/null, /dev/zero, etc, and additionally to any device passed directly to --bind argument like --bind=/dev/vcs. This won't work with USB because /dev/bus/usb is a directory.
To grant permission for currently running container named my_container (supposedly you started it with systemd-nspawn directly from command line) execute as root:
$ echo 'c 189:* rwm' > \
/sys/fs/cgroup/devices/machine.slice/machine-my_container/devices.allow
c 189:* rwm means read write mknod permissions for any character device with type (identificator) 189 and any subtype.
See also: https://kernel.org/doc/html/latest/admin-guide/cgroup-v1/devices.html
You can find type and subtype of device with file:
$ file /dev/bus/usb/002/002
This permission will only last while container is running.
If you are using [email protected] or want to persist permissions with it, create
/etc/systemd/system/[email protected]/override.conf
or
/etc/systemd/system/systemd-nspawn@my_container.service.d/override.conf
(depending on whether you want access to USB from any systemd-nspawn container or only from my_container correspondingly) with the following content:
[Service]
DeviceAllow=char-usb_device rwm
usb_device is an alias. You can find other in /proc/devices.
[1]: https://wiki.archlinux.org/index.php/cgroups