According to a post at TFW2005, the scene involves Sam "jumping from the ship to a building." A Don Murphy member and set extra sigma1 also claimed to know what the shoot was for. Of note is the invoking of Wheeljack ("Einstein") as a TF cast member but that remains unverified. Thanks to Udana for the link.
"The shoot involving the train derailed is called "Mayor's Mile" and is a continuation of the Chicago sequence. The scene itself will take place in Chicago within the movie. It involves the intro of a main antagonist, (which is the large construct with 2 turbines in the rear photographed earlier when Detroit production arrived). I won't reveal just yet who it is, but he will then transform and reveal himself to be orchestrating much of the chaos on Earth, most Autobots arrive (Bumblebee, Ratchet, Sideswipe, Wheeljack, and the Ferrari) to battle him. Prime, Ironhide, and Josh Duhamel are involved in another sub-plot that will be revealed later."