The audio played back in the courtroom is not the same as the conversation that took place earlier in the film. Notably, John Gotti used the phrase "physically sick" during the earlier conversation, but it does not appear when the tape is played back. Also when Gotti asks who "did the work?" Frankie says "Sammy," but on the tape, Frankie says "Fucking Sammy" which Gotti repeats.
When Castellano's driver and underboss, Thomas Bilotti, gets shot the blood appears on the outside of his coat but when the coat flies open, there is no blood or bullet holes.
When Frank DeCicco's car is blown up it is across the street, but it later appears in front of the club.
Paul Castellano tells Gotti and Dellacroce that he wants "one of his men, Ralph Galione" to get on the hit. According to Assistant U.S. Attorney, Galione was not one of his men; he was an associate at the Bergin Hunt & Fish Club, Gotti's club at the time.
There's a shot of Manhattan, which is supposed to take place in 1973, however we can see a building from the World Financial Center which didn't exist in 1973 and the antenna on top of the north tower of the World Trade Center which wasn't there at the time. This is clearly a shot of the Manhattan skyline as it looked in the mid 1990s.
In the scene where Paul Castellano is gunned down outside Sparks Steak House, the sign denoting the restaurant spells out "SPARK'S STEAK HOUSE" with an apostrophe. However, the real life restaurant has never had an apostrophe in its name.