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For some interesting info, while not actually canon, I believe one or two Ultra elites spawned from the IWHYD skull in Halo 2 wield Battle Rifles.
As for the Shotgun wielding brutes, they probably found them quite intersting, and wielded them, giving they were similar to their own Mauler weapons.
(A brute in the level uprising, on the chapter, Fight Club, can be seen, testing a human shotgun by shooting at a wall.)