Just been doing the 9:35am service Ronkonkoma - New York Penn, after leaving Jamaica station I was advised to stop at Woodside at 10:06. I thought nothing of it until I started to enter the East River Tunnel towards NY Penn. I’ve no idea where it went wrong as I don’t run the LIRR much but as I got further away from Woodside the distance marker went up. Sorry for the poor photo, it was quickly got while I was playing.
Woodside is the last station before entering the tunnels I belive (aside from long island city and Hunterspoint Ave, but they are both unused in service mode) It's definitely in the game as some services, the short ones, either start or end there back and forth to Penn, plus you can spawn on foot there. Looks to me like you've shot straight through.