This error can occur if the structure diffracts light to higher grating orders. The s-parameter analysis assumes that only 1 grating order exists in which case as you get far enough away from the structure the light will behave as a plane wave with uniform field intensity across the simulation region span. Metamaterials typically have a period which is much smaller than the wavelength of light so this assumption is typically good.
However if additional grating orders are supported, the fields will not have a uniform intensity. In this case, it is possible to modify the analysis script to calculate the S-parameters for only the zeroth grating order as discussed in this post:
The above post also discusses how to determine whether the structure supports higher grating orders.