RF Cable testing-- Ripples during S21 measurement
If your network analyzer is well-calibrated:

The reason for you seeing ripples is probably because there are actually ripples in the S21.

This might have different reasons; most likely, a non-perfect impedance match introduces reflections at the connectors, and that in turn leads to standing waves, which, for some frequencies will cancel out the signal (hence reduce S21) and for others overlay constructively.

But: without knowing a lot more, it's also totally possible that there's actual frequency-selectiveness in the cable, eg. by polarization losses in the dielectric. I'm not aware of any material that would have changing losses between 2.5 GHz and 3 GHz.