A simulation which has gone on as long as our species has been conscious would have a few features which would identify it as a simulation.
One, the current, established laws of physics would bend. If the purpose of the simulation is to test ideas, to test scenarios as to which are the most entertaining, which are the most life-sustaining, which are the most durable, then you would expect for all manner of societies to have been attempted, all combinations of leaders, all varieties of existence.
And, you would expect various tests of people’s reactions to different situations. Consider the Mothman Prophecies, by John Kael, with his extensive descriptions of strange visitors, observers with unusual behavior, taking down detail after detail of other weird happenings.
You might expect discontinuities in existence depending on where the observers were. You might expect the simulation to break down in remote areas, especially when other simulations were becoming increasingly energy intensive.
You’d expect the mathematics of super-string theory, describing reality to mirror internet mechanics, as Dr. John Gates suggested.
Considering the purpose of such a simulation – The Matrix had humans as batteries, but with the importance humans ascribe to entertainment and amusement, it seems equally as likely, if not more likely, that our actions function as a form of entertainment. The rise of reality television, and our use of simulations for entertainments (sim city, tamagotchis) (you can see that most of my references date from the nineties).
Yet, as simulations develop their own simulations, they become increasingly difficult to manage, with a great deal of computing power required to maintain their output. As computing power is exceeded, you would expect the reality to become increasingly outlandish, and such events as the inauguration of a comic-book supervillain as president of the US are inserted. People question the reality of such events, rightfully so.