This letter is devoted to point out a specific character of the Finite-Difference-Time-Domain method through the study of nano-structures supporting geometrical symmetry-protected modes that can not be excited at certain conditions of illumination. The spatial discretization performed in the FDTD algorithm naturally leads to break this symmetry and allows the excitation of these modes. The quality factor of the corresponding resonances are then directly linked to the degree of the symmetry breaking i.e. the spatial grid dimension even though the convergence criteria of the FDTD are fulfilled. This finding shows that the FDTD must be handled with a great care and, more importantly, that very huge quality-factor resonances could be achieved at the cost of nanometer-scale mastered fabrication processes.