Problems with Zigbee2MQTT have nothing directly to do with Home Assistant so you should really be posting such questions to Zigbee2MQTT’s community, either under their forum (discussions) or issues:
This Zigbee section in Home Assistant’s forum is really only meant for ZHA and Zigbee devices with it. Zigbee2MQTT is a third-party application and that includes that Zigbee2MQTT addon for Home Assistant.
Quick tip though is to check before is to check that root cause is not the same as for Home Assistant’s ZHA integration which is that support for commissioning Zigbee 3.0 devices via “Install Code” (or “QR Code”) has so far only been implemented for ‘zstack’ (Texas Instruments ZNP) and ‘ember’ (Silicon Labs EmberZNet) adapter type radios.
Other radio adapter types are either missing support in their respective adapter/driver for zigbee-herdsman or more likely missing in the manufacturer’s firmware commands/APIs and documentation.
So need to make sure have a newer and Zigbee Coordinator radio and firmware, meaning either a Texas Instruments CC26x2 based adapter or a Silabs EFR32MG2x based adapter with updated firmware. So preferably a USB dongle based on CC2652P or EFR32MG21, and update the firmware to latest recommended by Zigbee2MQTT developers.
Regardless you will need to provide logs as well info on exact Zigbee Coordinator and firmware to Z2M.