Numerical techniques for parallel dynamics in electromagnetic gyrokinetic simulations are introduced to regulate unphysical grid-size oscillations in the field-aligned coordinate. It is found that a fixed boundary condition and the nonlinear mode coupling in the field-aligned coordinate, as well as numerical errors of non-dissipative finite difference methods, produce fluctuations with high parallel wave numbers. The theoretical and numerical analyses demonstrate that an outflow boundary condition and a low-pass filter efficiently remove the numerical oscillations, providing small but acceptable errors of the entropy variables. The new method is advantageous for quantitative evaluation of the entropy balance that is required for obtaining a steady state in gyrokinetic turbulence.