Calculation of electromagnetic cross sections from surface integral equation simulations, a popular approach in microwave studies and recently also in optics and plasmonics, requires only a single post-processing step, which can, however, be very sensitive to the precision of the simulation result. We investigate the accuracy and robustness of two methods for cross section calculation, displaying when and why errors may occur, in certain cases even unphysical behavior. A calculation recipe which avoids unphysical results is given, ensuring convergence of all obtained cross sections. This study will help judge the accuracy of performed simulations and can prevent misinterpretation of modeling results.