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Hi Saar,
Bloch BCs are set to a single wavevector, so a change in frequency will have an angle offset. Since you are looking at different frequencies, I think this is why the grating orders are not in the corresponding angles. This should have some more information to help you: Bloch BCs in broadband sweeps over angle of incidence – Ansys Optics
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Likewise, since you are looking for a generated response, you might need to be careful about the input field and make sure that you are not including your second harmonic frequency in your input.  This page might be helpful in this regard: Harmonic generation with a chi2 material – Ansys Optics