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That discrepancy was fixed with a ret-con to the lore, and the Brotherhood of Steel has been added anyways in a nascent form that fans had never seen before.
However, Bethesda did get off on the wrong foot for many Fallout fans, as the series' lore dictates the Brotherhood of Steel wouldn't exist when Fallout 76 is set. With how popular the Brotherhood of Steel is, there was a lot of pressure on Bethesda to do it justice, especially with how contentious Fallout 76 has been during its release and the years since. Now, the faction's updates have come and gone, bringing closure to the Brotherhood of Steel storyline and leading many fans to start comparing the game's version of the faction to previous iterations.
As the primary focus of multiple updates, the Brotherhood of Steel now plays a pretty large role in the ongoing story and politics of Fallout 76. The Brotherhood of Steel is one of the most iconic factions in the entirety of Fallout, so it's no surprise that the organization eventually made its way into Fallout 76.