When I stop at the Bronx bridge marker, it disappears but doesn't trigger the next one while the HUD still tells me to stop at the Bronx bridge.
Hmm, I'm having pretty much exactly the same problem whilst doing the Fresh Pond Junction transfer over to Oak Point Yard, I got to the part where you have to reverse into a siding and couple up 10 cars. I did this, they coupled fine, but then, when I jumped back in the driver's seat I noticed the blue marker with the star was still there at the coupling point and I still had a message on screen telling me to couple up the ten cars. So I walked back to the coupling and the blue marker was like 3 metres in the air. I have absolutely no idea what I was supposed to do. I uncoupled and re-coupled, tried driving away a bit and adding a touch more speed when backing into the cars, even drove 500 metes up the track and then reversed back. Nothing worked so I was unable to continue the scenario. Don't know if it is a bug, but up till then I had done everything in the correct sequence, so basically, I ended up having to quit it if the game. I will try again, but I wasted quite a bit of time trying to work it out so it'll have to wait. Most annoying.