This is how lots of new science is discovered. One example is the Theory of Relativity. Sure it was not a software simulation per se but it was still simulated on paper. It was not confirmed by experiment until several years latter.
If I'm not mistaken I think what OP is referring to is an apparent emergent phenomena that contradicted theory, whereas I believe GR was discovered through theory (ie Einstein's "happiest thought" was in an elevator shaft).
