Hi Handon,
I believe the issue is that the simulation reaches the end of simulation time before the auto shutoff level is reached. FDTD is a time-domain approach. The results are then converted into frequency domain by using the Fourier Transform. For the fourier transform to be accurate, it is important that the fields decay sufficiently at the end of the simulation. If not, you can obtain inaccurate results and a typical indication of this issue is the ripples you see in your spectrum.
Please check the status of the simulation after you run the file.
If the status is 1, it means that the simulation ended before reaching the auto shutoff level. If that is the case, increase the simulation time by 10 times and rerun the simulation.
Regards,
Amrita