When stopping at stations on the East Coastway line, passengers will not board or de-board the train. I'm not sure if this happens on every service, but so far I've played a couple of them and it has happened on every single one.
Is this on service mode, not on the scenario planner? As i've personally not experienced this issue on ECW service mode but it may be platform or service specific issue. You're not by any chance opening the doors before it gives you the prompt to do so, as that usually causes the passengers to not board or alight.
Passengers not getting on or off the train happenes on most if not all the passenger routes in tsw2 which is a joke in my opinion