I have/had the same issue happening in my project, where I just recently activated Scene Graph.
As the usage of Scene Graph in my project is still very limited I could quickly pin down the error being only present, when I subscribed to one of the Tick Events(PrePhysics/PostPhysics). As soon as I remove the subscriptions, the Hot reload error is gone.
I am not sure if this is really the underlying issue, but thought I would let you guys know my observation.