If data is used to gauge the background levels, it means that the particular quantum mechanical models used in the simulation events are unnecessary in order to extract a significant signal. It does not depend on dynamical assumptions that exist in the generators of the monte carlo events, which vary in how well they desribe data.
For example in this "Search for the Standard Model Higgs boson"
Most background shapes are taken from simulation and normalised using control regions in data except for multijet, which is estimated entirely from data,
It implies that the multijet simulation is not well fitted, so where jets are important in the analysis, data of multijets are used to estimate the background.