Dear Mehmet
As I see, you are analyzing using Hyperlynx ver 9.0. This has a different simulation engine from what was used in Hyperlynx Ver 8.0 used by the instructor in the training module. This kind of aberration was experienced by me also when same topology when analyzed in Ver 8.0 had different waveform. I replicated the same topology as you have shown in version 9.3 and observe that the waveform are identical to what you saw. EMI analysis showed the results similar to what the tutorial says. I could not understand your concern here.