There are several things you need to be aware of. First of all, there are some very common causes for Zigbee problems, such as not using an extension cable to connect the coordinator to usb, channel choice and lack of zigbee routers. Fortunately there are also comprehensive troubleshooting guides. Two links below.
One thing in particular relating to the advice above: if you keep the hue bridge for all other zigbee stuff, then you have two separate zigbee mesh networks that do not talk to each other, but may interfere with one another (if they are on the same channel). It also means there may be too few zigbee routers in each mesh network.