Ascended Fanon: The Deimos Clan Heavy mech was originally a non-canon mech introduced by Mektek's free re-release of MechWarrior 4: Mercenaries. It was later made canonical with the release of Technical Readout 3085
Development Hell: Handbook: House Kurita, and to the lesser extent Interstellar Operations.
Real Life Writes the Plot: The reason why the Eridani Light Horse mercenaries were killed off, and in really gruesome way for that matter (Left to die in the in the crossfire of two clans). The longer version: Someone wrote a fic about the ELH backstory, and due to various circumstances, that fic was canonized by accident without paying the author. The fanfic writer sued, and the case would go on and off for nearly a decade until the developers, already wary after the Unseen debacle, decided it was not worth it and got rid of ELH.
Screwed by the Lawyers: Thanks to some SNAFU with the licensing, several of the original BattleMechs (based off of 'Mechs from various Japanese anime and manga) are now considered Unseen.