I was able to resolve the issue.
It seems to have been related to how i mapped the device into the container.
Before:
privileged: true
/dev/serial/by-id/usb-Nabu_Casa_ZBT-2_%serial%-if00:/dev/zigbee
After:
/dev/serial/by-id/usb-Nabu_Casa_ZBT-2_%serial%-if00:/dev/ttyACM0
My guess is that with privileged: true, the container already had access to the adapter, and the additional mapping exposed the same device a second time as /dev/zigbee.
That probably caused the adapter to be detected twice and led to the issue.