There has always been at least some specs in the game that didn't have a proper simulation, because of an in-game bug, an improper coding or a lack of community backing up the spec.
As said earlier, SimCraft is as good as the people coding for it, so there may always exist some discrepancy between simulations and actual results.
During Cataclysm, I used to perform better than my sims and, IIRC, it was because both the rend-clipping bug and the possibility to have some 4-GCD CS weren't handled by SimCraft.