- Broken Base
- Ensemble Darkhorse: Lord Infamous, and to a lesser existent Gangsta Boo, and Koopsta. So it's no surprise that when they left the group they took a few fans with them.
- Everyone Is Satan in Hell: According to some Moral Guardians. They brought it on themselves though, with their Satanic lyrical content, with at least one song questioning God, and their name subtly looking like "666 Mafia", as well as the song Stay Fly" where a sample from the Willie Hutch song "Tell Me Why Has Our Love Turned Cold" was misinterpreted as "Lucifer, you're my king, you're my father" instead of "you're my pride, you're my king, you're my father", as if the Three-Six was indeed singing praises to the devil. They of course deny this.
- Fandom Rivalry: with Bone Thugs-n-Harmony fans. To a certain degree they share a small portion of their fan base.
- They Changed It, Now It Sucks: Fans resent the steadily gradual shift from their gangsta-horror, death rap edged style, to a more generic gangsta rap, and eventually to just light Hardcore Hip Hop. Their production is the only saving grace in some fans eyes. Even then people still hate the "lighting" up of their dark eerie moody beats.