For every action taken inside the simulation, there will be things that happen on the "hardware" outside of the simulation and since it's simulated, not real, the "hardware" won't respond in precisely the same way as it would if it were actually real in every possible circumstance.
The only simulation that would respond in exactly the same way as a "real" universe under all circumstances has to be a perfect 1:1 mapping in terms of "universe hardware", which is exactly the same as running on "real" bare metal.