It sounds like the yellow bus was run by the port for passengers to safely navigate the port area. These buses usually have nothing to do with the cruise ships and run on their own schedules. It does sound unfortunate that everyone had to stand in the rain. Plus HOHO buses have to stay on their time tables, as well. Yes, Destination Services should have contacted the Port Authorities to get an idea of the particulars on navigating the port area for those who wish to go out on their own.
Glad to hear that you had a good rest of your day and enjoyed a lovely meal.