Blizzard has posted hotfixes, which included a fix for Naxxramas in Classic Season of Mastery addressing bonus loot.

Season of Mastery


Fixed an issue where bonus loot could not be rewarded when defeating a boss using Runes of Fortune.
Developers’ note: Raid groups should always receive an extra Set Piece Token, piece of Gear the boss normally drops, or Splinter of Atiesh per stack of Rune of Fortune the raid has active.

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