I couldn't recall seeing the Gotham monorail system in this film and Wayne Enterprises weren't located in Wayne Tower but in some ordinary skyscraper with "WAYNE" written on it. What happened? Well here's hoping they'll get to make another one.
Themonorail can be seen in the background of a couple of shots, including the one with the black Wayne building. It is not explained, but one can assume that after the events of Batman Begins, Wayne Enterprises moved its corporate offices out of Wayne Tower, which can also be seen in at least one background shot.