A total of five days was spent filming in New York City. The two major problems faced by the crew were the weather (It rained for most of the shoot.) and the popularity of Frank Sinatra. Gene Kelly explained that the movie was filmed at the height of Sinatra-mania, and Frank would be instantly recognized by people on the streets. To avoid crowds, the cast insisted on taxis instead of limousines for transportation and that the camera be hidden inside a station wagon. During the finale of the musical number "New York, New York", which takes place in the sunken plaza at 30 Rockefeller Plaza in front of the statue of Prometheus, the heads of hundreds of curious spectators can be seen at the top of the frame of the last shot, staring at the three stars over the wall behind the statue.
There was a real-life version of the "Miss Turnstiles" contest in New York City. "Miss Subways" was a beauty contest run by the New York Subways Advertising Company from 1941 to 1976. Subway cars featured posters of pretty young women who lived and worked in New York.
According to information contained in the file on the film in the MPAA/PCA collection at the Academy of Motion Picture Arts and Sciences Library, the Breen Office refused to allow the use of the word "helluva" in the song "New York, New York" [it's a helluva town]. MGM later changed the word to "wonderful".
Ann Miller commented in a TCM interview that at least one take of her big tap number to "Prehistoric Man" was ruined because of her own costume. She had been dancing very close to the large dinosaur skeleton and, during a series of her trademark tap spins, the flared skirt she was wearing brushed against some of the bones and brought the entire exhibit crashing to the ground. Filming was halted for a considerable time while it was put back together.
Frank Sinatra, who was very thin, had to wear prosthetic padding to fill out the seat of his uniform. In a TCM interview, Ann Miller said that Sinatra was extremely sensitive about his padding and did not appreciate the usual movie set horseplay involving his lower half.