But if the computer could detect the issue and slowdown or pause the simulation, ask for an administrator to intervene and then resume the simulation the issue would appear solved.

In Trek tricking the crew fails either because the simulation is imperfect or because it is to slow and fails to do high computation but the crew tricked Moriarty because he is a computer program and they can pause or slowdown his simulation and handle exceptions.

I recommend watching the movie Inception, it also has the idea that you might never be sure if you are in reality or stuck in some simulation.