Hello Debashish,
You need to narrow it down to 1 of 2 possiblities.
1, the simulaiton is correct, but fft is providing the wrong results. In this case, it can be easy to have a bug in the script written to generate an FFT. Are you writing your own script or using existing tools? I suggest starting here for FFT analysis: https://www.mathworks.com/help/physmod/sps/powersys/ug/simulating-variable-speed-motor-control.html#f1-11898
2, You are using fft correctly, but the simulation is wrong. Are you able to share your model for it to be looked at for potential issues? Can you share your fft results that are showing this unexpected behavior?
Regards,
Joel