On Peninsula Corridor with the Baby Bullet installed, service 143 gets stuck at a red light just before 22nd Street. There are 2 trains in front of the Bullet, both F40PH sets, one being the "special" consist with extra cars and 2 locomotives, both of which are stuck. The middle one (in front of me) is stuck at a signal, but the one in front is just sitting stationary at the switch to the 3rd track just outside of the tunnel. It looks like the train is supposed to diverge at the switch, but in-game the switch is set to go straight. There is no way around this bug, and it breaks the game on this particular service.
The only workaround for this is temporarily uninstall the MP 15 complete service 143, then reinstall the MP 15 if I remember correctly