I can no longer avoid to put a hero in a ship, when moving a hero with other land units onto a port.
Previously, one could select the up arrow for heroes on port to have the hero not to embark into his own ship, but instead ride on another ship or flyer or sea creature (see http://www.warbarons.com/wiki/martimtravel for details).
See game id 41295 (this game is not a serious game, it is just for experimenting around): two heroes are located on ports with other land units, but neither hero can be disembarked.