As long as you are using a waveport, be sure the excitation plane is on the edge of your simulation. A waveport is a port that simulates an infinitely long waveguide as the source. Could you include a picture of your simulation thus far? If you have vias or slits, then I would think you would want to include an airbox larger than your waveguide and assign there a radiation boundary.
As far as your error, I'm pretty sure you shouldn't get an error for the conductor being shorted elsewhere, that would prohibit simulating a lot of common structures. You probably will get an error without an integration line leading from one conductor to another on the plane of your excitation.