This warning is issued when the radiation boundary condition, PML or Approx Open, is not a fully closed surface.
For the best accuracy in antenna far field calculations, the radiation boundary condition should be a closed surface with no breaks, except for intersections with PEC ground planes or symmetry planes. This warning will be issued any time Analyst detects another structure on the boundary.
Some geometries can be accurately defined with structures or ports on the simulation boundary, as long as only very low fields are radiated in the direction of the boundary structure. You should use great care when defining such structures, because they may invalidate the far field calculation if they interfere with the radiated fields too much. For instance, rather than define wave ports on the simulation boundary you will get better results with internal wave ports, as described here for wave ports on traces, and here for waveguides.