dear maryam, i am working about periodic structures. and when i want to simulate a unit cell, i do it by hfss. when i simulate a unit cell by cst, the phase is incorrect. so, i suppose you, simulate your unitcell by hfss again.
and use floq port. and notice about the deemed distance.
If it is S11 then you have almost total reflection anyway - so you are probably doing something else wrong, unless you are looking at the reflection to try to estimate the loss.
If there is not much loss but a poor match the signal can bounce about in the simulation for a long time and then rounding errors become significant and you can get more energy coming out than you put in! Perhaps you are trying to simulate a high Q resonator to get the loss. The time domain solver is not a good way of doing this. The frequency domain solver is the right one for problems like that.
I heard that Time domain approach is not good for scattering problem of a Graphene based structures in CST, So probably frequency domain one must be correct.