- Banned in China: Some Northern Irish politicians asked 2K Games to pull the game out from stores for glorifying the IRA due to during one point in the game, Lincoln helps one of his allies, Irish Mobster Thomas Burke, steal some cars for him so he can send it to his friends in the IRA who will turn those cars into car bombs in their bombing campaigns against the British government and Burke's home turf has graffiti of the Northern Ireland flag vandalized with the words "Traitors" written over it. Burke also expresses anger towards Loyalists, who he claims are "putting down good Catholic citizens". So far, 2K Games have not responded and the game is still selling since pulling the game out from the stores would defeat the game's message on how bad the 1960s were for everyone and the fact the whole IRA thing was a cover up story as Burke is actually selling the cars to leave some money for his daughter once he dies.
- Development Hell/Troubled Production: Hangar 13 suffered from many things during and after the games production, including (but not limited to) having to design the game while building a new game engine, cultural clash from the American and native Czech employees, fitting many things in at the last minute, the bugs that ensued from being an open-world game rather than a linear game, and many of the game designers leaving, some of which moved to different studios, left voluntarily, or had to be let go. Despite their ambitions, the game's mediocre reviews was a catastrophe for Hangar 13, causing a mass amount of unemployment and having to move back to the Czech Republic. Since then, they've remained quiet with no new game ideas planned.
- Name's the Same: Judge Cornelius Holden shares his title and last name with the infamous main antagonist from Blood Meridian.
- What Could Have Been: The original prologue was supposed to involve Lincoln Clay shooting a cop, thus explaining why he went off to fight in Vietnam. Hangar 13 not only cut the prologue but deleted it from their servers, fearing that, taken out of context, it would've been ammunition for Moral Guardians to claim that the game was about an Angry Black Man who goes around killing cops.
Trivia / Mafia III