In the beginning of the Avengers movie with the Black Widow scene, the scene takes place in Russia with Norfolk Southern locomotives going by on the far right corner of the warehouse in Cleveland, Ohio where the scene was filmed. Of course the NS logos were blacked out and were replaced with some Russian letterings.
Also, in The Dark Knight Rises, the scene where Detective Blake goes to the cement factory, a CSX YN2 engine shows up pulling autoracks with their various logos on them. But when the locomotive comes out from behind one of the cement trucks, the scene gets cut and the CSX logo is only partially seen. The scene takes place in Gotham city but is filmed in Pittsburgh so that is probably the reason why Christopher Nolan did not want anyone to see CSX in the film.
