Three typical algorithms of Pauli blocking in the quantum molecular dynamics type models are investigated in the nuclear matter, the nucleus and the heavy ion collisions. The calculations in nuclear matter show that the blocking ratios obtained with the three algorithms are underestimated 13-25% compared to the analytical values of blocking ratios. For the finite nucleus, the spurious collisions occur around the surface of the nucleus owing to the defects of Pauli blocking algorithms. In the simulations of heavy ion collisions, the uncertainty of stopping power from different Pauli blocking algorithms is less than 5%. Furthermore, the in-medium effects of nucleon-nucleon ($NN$) cross sections on the nuclear stopping power are discussed. Our results show that the transport models calculations with free $NN$ cross sections result in the stopping power decreasing with the beam energy at the beam energy less than 300 MeV/u. To increase or decrease the values of stopping power, an enhanced or suppressed model dependent in-medium $NN$ cross section is required.