The nonlinear propagation of EMW in periodic media is of great interest due to the possibility to accumulate energy in periodic media within the stop band and, therefore, the input intensity levels for observation of nonlinear phenomena are quite low [1]. For resonant interactions, also it is possible to realize matching conditions, which are not possible in uniform media. Both resonant multiwave interactions and selfaction of EMW in nonlinear periodic media have been analyzed [1, 2]. Also, a method based on a slow variation in time was proposed, which seems more adequate than others based on coupled equations [3]. The presence of defects in periodic structure leads to narrow regions of transmission within the stop-band. In this case, the application of coupled equations for counter propagating waves becomes doubtful, and a more general approach is needed [3]. Also, the influence of defects on the dynamics of modulation instability of long pulses is of a great interest. The present paper considers numerical simulations of the pointed above phenomena. For a correct description of the nonlinear dynamics, it is necessary also to take into account the wave dissipation and possible transverse diffraction. The results of simulations demonstrated the essential influence of defects within the periodic structure on the nonlinear propagation of EM pulses, even if the carrier frequency is chosen within the stop band of the structure with a defect. This fact can be explained by a quite wide spectrum of the input pulse, and the “tail” of such a spectrum is within the transmission region due to the defect. This situation is analogous to the nonlinear propagation of short spin-dipole waves in the vicinity of the cut-off frequency [4]. The dynamics of modulation instability also changes in the presence of the defect. The diffraction can affect essentially the modulation instability dynamics.