Both.
The description of the detector is not perfect: You never get the radiation length of every component exactly right, you never know the exact asymmetry of your detector in response to kaon/antikaons, you don't get the exact amount of charge sharing between adjacent channels after radiation damage right, and hundreds of similar details.
The simulation of the proton-proton collisions is not perfect. This is mainly due to nonperturbative QCD effects. You don't know the parton distribution functions exactly, the hadronization description is not perfect. In addition, you have to limit the calculations of some processes to fixed order, and so on. There are processes that can be modeled very well, while others don't have any purely theoretical predictions and rely on experimental data.