Running on Snow Leopard under Crossover (which might be the real source of the problem):
I had removed all but one ship from a deployment. I was dragging the last ship off the map and I seem to have dragged it over the “Add Command” option. The new command window came up but there were no ships in deployment and the popup would not accept cancel or any other clicks. Escape also didn’t work. Finally had to kill the game.
I’ve not been able to reproduce the issue so it may be a crossover problem.
Just wanted to report it in case someone else has something similar.