Need more information. What is termination type, what software?
When using two identical ports if waveguide length is multiple of 180deg, then you may obtain good S11/S21 even in unmatched configuration, because impedance repeats each 180 deg. I often perform two simulations for microstrip/waveguide structures: first - original design, second - original design with additional 90deg line/extended waveguide length. If something is unmatched this 90 degree reveal it by doing transform.