I'm a little bit confused. Have Mysensors set up with RPi MQTT gateway.

I have launched mycontroller and disabled MQTT broker. Instead mycontroller connects to my MQTT server.
My whole set up is connected to Home Assistant. So i wonder if this set up can be ran safely as i have noticed some erranous behaviour (nodes not reporting back to home assistant) until i stop mycontroller. Any other options to disable so everyone can exist on the network safely?