I think it has to be set in the node causing the problem. However as has been stated, it is just a warning so you should be able to ignore it. It is likely from one of the config nodes which is why disabling the flows does not stop it.
Well for now what seems clear that arduino node is giving problems, during restart the pi at the begining it connected to the board as I see the relays switching but later on is not working.
If I go to the flow I see connecting and there is no way to make it work even trying to configure again the port.
However If I remove the usb cable from the pi and plug again (that makes force to change the port from usb0 to usb1) then I change the port on the config node and deploy, then it works again.
To start seems latest 0.2.2 is in trouble with the usb serial port.
From other side and less important even not having connetion of after unplug/plug usb cable and change the port on config node + reload page always shows outputs as connected and inputs as connecting.
Well, after many trials and attemps I think I have the clue....
I originally thought it was related to the serial port as apparently loads for a second after service restart but then is gone...node-red-node-serialport but after testing found no difference.
The point is with node-red-node-arduino versions 0.1.0 or previous it works fine, with 0.2.2/0.2.1 or 0.2.0 it has a problem, I see relays making a blink at service boot up what means it connects for a moment but afterwarts is gone and does not connect anymore.
If I diconect usb cable and connect again so raspi reassign to port usb1, I change it on arduino config node and restart it will work at deploy, but as soon as you restart service again it will be again failing.
Hope that helps someone else, for now I remain at 0.1.0 npm version, proceed with>
npm install node-red-node-arduino@0.1.0
note I have latest version up to date for everything
By the way, if you want to track down that listeners issue, try turning up the Node-RED logging level in settings.js. It produces a shed-load of output but should let you see what Node is loading when you get the error.