That warning is not really a problem (unless of course you hate seeing warnings)., In the Graph.UpdateGraph method (which is called from MonoManager), we first check to see if the graph still “isRunning”. If so we continue executing the graph, otherwise the warning is logged. Checking the “isRunning” flag is exactly so that it accommodates the fact that UpdateGraph will be called from MonoManager due to the reasons you stated, without having to resolve into more complex solutions.
I could remove the warning from there (which was only added recently), but the actual behaviour will remain the same (hence without a harmless warning logged 🙂 ).