This is an old age frustration that has probably been forgotten. I will place a reminder that it exists still and hope it can be resolved. The issue exists in the latest version of the game where you can see passengers on board when moving out of a storage yard into a station to pick them up. There has to be something that can be done. Also when the train has finished it's run and heading back to storage it must not have anyone on board.
It really is quite annoying that depot trains have passengers in them. I'm really hoping that perhaps it could be fixed with the Rush Hour update, since it's dealing with passengers.
This actually isn't a bug. Passengers just haven't been programmed to be smarter. Hopefully this changes with Rush Hour, although the main focus is to have more passengers at stations and having much more diversity in passengers. But I wouldn't be surprised if they also make passengers smarter as well
It's so creepy when you end up in Gilligan Depot and people stare out of parked, dark trains you drive past. Really