How did Joanna know what was going on?
She seemed to be keeping close tabs on what Michael was doing, even complimenting him on his creative method of escaping the state troopers and climbing back onto the train. Maybe it was something really obvious that I missed, but how was she observing all this? Was that ever explained? I know she had one additional "agent" on board the train, but I don't think he was always present when it seemed like Joanna was watching Michael's every move. Maybe she tapped into the security cameras on the train, but #1, I don't know if that is technologically possible and #2, I'm pretty sure they didn't show that happening.
This sort of brings me to my only major complaint with the movie. If Joanna's organization is so powerful and well-connected that they were able to orchestrate this elaborate setup and even assassinate a random pedestrian without fear of their agent being caught, why involve Michael at all? I know, I know, then we wouldn't have a movie, but from a writing standpoint, it just seems like Joanna's people would have been quite capable enough of doing this on their own.