The nodes (corner points) of your beams are outside the column, so the program gives a warning. (Your beams pass through the column, they are not connected to the column in the analysis model, you can see the deformations by examining the deformations from the 3D analysis model). When you convert your column to a rectangular column, the program does not give a warning because the corner point remains inside the column. If you move the beam ends to stay inside the column, there will be no problem.