It may be that you’ve reached a limit with regards to a repeater. While you can have thousands of Zigbee devices, you also must have a mesh with enough repeaters to handle all those devices.
There’s a discussion around here somewhere that specifies how many battery powered devices can join directly to the hub, as well as repeaters, before you need to start adding more repeaters to your mesh.
If you don’t have any repeaters, that may be your issue. If you have repeaters, attempt the join process really close to that repeater device.