While the film was praised at release for utilizing real recordings and TV appearances that were replicated wholesale, the plot also plays very fast and loose with the chronology of certain events, to the point that it could be described as Very Loosely Based on a True Story.
- The scene where Neil Dellacroce, bothered by Don Carlo Gambino picking caporegime Paul Castellano over him, goes to Gotti at his bar and breaks the news to him (causing Gotti to fly into a rage as neighboring FBI agents observe from across the street) was completely fabricated for the film. At the time of Gambino's death, Dellacroce was jailed for tax evasion and couldn't intervene or contest the succession, though he would be released several weeks later and appear in person for Castellano's confirmation on Nov. 24, 1976 — a meeting that was shown in the film. Conversely, the real-life Gotti was also jailed at the time Castellano was confirmed (for the Galione murder) and wouldn't be released until July 1977, nearly a year after Castellano had taken over the family.
- Sammy Gravano is shown killing Nicholas Scibetta, an associate of the family, via ambushing him in a warehouse and using a weapon that repeatedly jams while Scibetta begs for his life. The real-life Gravano never killed Scibetta, based on the known reports (Gravano himself alleges two other hitman committed the deed), and was so angry about Castellano ordering the hit that he initially wanted to kill Castellano himself before being calmed down by Frank DeCicco. Scibetta was also Gravano's brother-in-law, a fact that is actually referenced towards the end of the film by Gotti during their conversation in the holding cell, but Gravano himself never displays any remorse about killing a relative.
- Neil Dellacroce is shown passing away in bed shortly after having a heart-to-heart conversation with Gotti, and guarded by Gotti's crew in his home. In reality, Dellacroce died at the (since-shuttered) Mary Immaculate Hospital in Queens and had been indicted a week earlier (along with the heads of New York's Five Families) via the Mafia Commission Trial, a fact that is never referenced within the film itself.
- The setup for the Castellano hit is greatly changed from its real-world incarnation. In the film, Gotti and Gravano make plans to kill Castellano long before Dellacroce passes, but only agree to wait until the latter had died of natural causes before making a move out of respect. In real-life, a number of factors, including Castellano refusing to say goodbye to Dellacroce (which is referenced in the film, but made to be the point of no return), Castellano making his bodyguard Thomas Bilotti (a dimwitted enforcer with no diplomatic skill) the new underboss, Castellano's heavy-handed approach in running the family (specifically, he demanded more from the blue-collar crews than what they could offer, wanted to steer the family towards the white-collar rackets, and most of his soldiers felt he was too isolated), and Gotti getting word that Castellano was threatening to break up his crew, all played a part. Additionally, Gotti didn't approach Gravano with the idea to assassinate Castellano, only coming to him with it (by proxy) through Angelo Ruggiero first (which is never shown in the film).
- The circumstances behind John Favara's disappearance (and presumed death) are largely fabricated for the film, with no clear answers even decades on. In the film, Favara has a My God, What Have I Done? moment when he realizes he's hit and killed Frank Gotti (who was on a bicycle) with his car — the real-life Favara instead began ranting and raving towards a crowd that had assembled, asking them why Frank was on the street to begin with, and whose family he belonged to. While Gotti is shown to have not requested reprisal against Favara as shown in the film (even pointedly ordering Gravano to let it go), Gravano and another associate ambush and kill Favara in a roadway underpass before fleeing the scene. In actuality, Favara was never found, and it was alleged in documents filed by Brooklyn prosecutors in 2009 that mob hitman Charles Carneglia (one of a group of seven hitmen dispatched) killed Favara and disposed of his corpse in acid.
- Shortly after Frank DeCicco is killed by the car bomb, Gotti visits the (now-retired) Joe Armone for advice. Armone criticizes him for Tempting Fate and more-or-less indicates that he's not a fan of the way Gotti operates, indicating that he "held (his) nose" during the Castellano assassination and Gotti's subsequent ascendency to the role of boss. This is counter to his real-life portrayal, who didn't care much for Castellano and regarded Gotti's plan as his last chance to get a leadership role within the family. Armone was also appointed underboss (until his arrest in 1987) after Gotti took command of the Family, a fact that is never remarked on in the film (Gravano is regarded as the underboss for the entirety of Gotti's tenure).
- In the film, the assassination attempt against Gotti (the rigged Buick) occurs seven months after he's elected as the new boss of the family, and kills both Frank DeCicco and another Gotti capo, with Gotti having reason to believe that D.B. has something to do with the hit (due to him being absent from a high-level meeting with the rest of the capos held immediately afterwards). In reality, though, the hit only happened four months after Gotti took the reins, DeCicco was the only casualty, and unlike the film, the Gambinos knew exactly who did it — Vincent Gigante, the boss of the Genovese family, and a character who was Adapted Out of the film. Due to the film being a Compressed Adaptation, D.B.'s murder is implied to happen almost directly after the assassination attempt, whereas in reality, it occured three months afterwards.
- Robert D.B. DiBernardo's murder takes place in a different location (the ground-floor offices of Gravano's drywall company, as opposed to the basement) and is extended (Gravano and D.B. toast before he is killed in the film, whereas DiBernardo never received his coffee in reality; Gravano offering D.B. coffee was the signal for him to be killed). Additionally, he is shot from behind by Joseph Paruta with a .380, whereas in the actual version of events, Paruta outfitted the gun with a silencer before shooting DiBernardo.
- The scene of Gotti visiting Ruggiero, who is in a withered state due to terminal lung cancer, in a hospice in 1989 and sharing cannoli with him was made up for the film. In reality, Gotti refused to visit Ruggiero, as he considered the latter to be a liability due to him being recorded by the FBI despite being urged to do so by Gravano and Gene Gotti.
- The arrest of Locascio, Gravano and Gotti at the Ravenite is played up with a far more hostile atmosphere than it was in reality as Gravano later admitted in his "Our Thing" podcast. Whereas the cops confronted the group of mobsters within the club and there was a standoffish atmosphere in the film, the actual incident was far more relaxed with Gotti acting sheepish and joking with the officers, and the trio being allowed to share a final cup of coffee in the Ravenite before being led out. Unlike the film, Gravano and Gotti were not placed in the same car together — they were each led to separate cars, while the arresting officers later joked to Gravano that they were doing it for show and took the handcuffs off of him after they got him into the car.
- The film portrays the FBI agents as being practically giddy over playing the incriminating Gotti recordings in court. In reality, the prosecution was forced to reveal the recordings to Gotti and Gravano early after a judge refused to go along with the prosecution's case that Gravano was a public threat, reasoning that Gravano had acted as a model defendant in the past and showed up punctually to a prior tax evasion trial, thus forcing the prosecution to play the tapes early.
- Gravano is shown making the decision to flip on Gotti after what appears to be a single night's (or weekend) lockup in a jail cell, where Gotti only reasons that it's because of his own vision that Gravano got as far as he did. In actuality, nearly a year passed between the first bail hearings (where the tapes were revealed) and Gravano's eventual decision to turn state's witness in late 1991.
- Gravano's decision, as revealed by him in an interview, was due to John's refusal to accept his mistakes, his escalating mistreatment of both Gravano and Locascio, and Sammy realizing that Gotti was setting him up to be the fall guy, and attempted to deny him access to the audio transcripts (which, unlike the film, he never heard prior to him agreeing to turn on Gotti). The tipping point for Gravano was when he and Locascio vowed to have John taken out and for Sammy to become boss, only for Sammy to realize that he would also have to kill potential rivals in order to prevent any retaliation, which sickened him to the point where he decided his only other option was to flip.
- Gravano tells Russo, Mouw and other FBI agents that once word of his cooperation goes public, his wife will divorce him (and he comments that he'll have to functionally cut all ties to his previous life). This never occurred during the real-life trial — Debra did divorce Gravano, but only in 1996 (the same year of the movie's release). Even then, she partnered with him on the drug trafficking activities until he was incarcerated in 2000.
- One of the final scenes in the film shows Joe Armone reacting in sadness in his coffee shop after watching the live verdict during Gotti's trial in mid-1992. In real life, Armone was long-imprisoned by the beginning of the same year (having been arrested in 1987, as noted above) and died of natural causes on Feb. 23, 1992, nearly two months before the verdict was read, making this both a case of Spared by the Adaptation (Armone is not shown to be ailing in any way when he's last seen) and Karma Houdini (as he's not under any legal scrutiny).
- At the end of the film, Gotti and Locascio are found guilty of all charges on Apr. 2, 1992, and summarily sentenced to life without parole with Gotti seemingly being remanded immediately and sent to a federal prison directly after the trial. The real-life trial took far longer, with the verdict not being read until June 23, 1992, Gotti being served a $250,000 fine in addition to the life sentence, and Gotti officially surrendering himself to authorities nearly six months later, on Dec. 14, 1992.
