Towards the end of the movie, when the policemen are boarding the train in Newark, the film has been mirrored, as can be seen by the word "PACIFIC" (as "CIFICAP") on the right side of the door.
While the premise of the film has the main characters traveling via train from southern California to Newark, NJ, the film was in fact filmed entirely in southern California. In 1959 the Union Pacific Railroad did not offer passenger service east of Chicago. This is apparent during the final chase/fight scene between the two main characters. In the background, they are seen running through a rail yard with Southern Pacific and Union Pacific engines.
Although the finale is supposed to take place at the train station in Newark, New Jersey (as of 1959, Penn Station), the passenger platforms at Penn Station are elevated, so passengers would not use stairs to deboard the train. At the finale, the platforms are at ground level, showing that it clearly doesn't take place at Penn Station.
The finale of the film, in which Gregg Palmer chases Ed Platt through the railyard and factory, is supposed to take place in Newark, New Jersey. However, they are clearly on a Union Pacific train, which had no passenger service beyond Chicago in the late 1950s.