I think you mean "cut off" frequency instead of "resonant frequency".
Althouh it is not very usual, sometimes it is useful to have degenerate modes in our design. For example, in a rectangular waveguide with square section, the modes \[TE_{01}\] and \[TE_{10}\] are degenerate. Exciting these two modes with a 90º phase shift is a useful way to produce circular polarization.
The most common EM software produce a warning in case you have a port that can support degenerate modes or multiple modes. You can separate multiple ports by modifying the number of modes, and you can separate degenerate modes by expliciting the mode polarization.