I have Naxxramas missing Sapphrion even though I have Kel Thuzad beat 5 times. Firelands only shows Normal completed, not Heroic. I did Trial of the Crusader after Firelands and it updated after logging out, but nothing else has. I am sure some others are wrong as well. I am currently going back and making sure I have done them, so I may find more that are not correct. This seems to be an ongoing issue.
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I raided through WotLK, so I have around 50 kills on every other boss in Naxx, but the armory shows 0 for Sapphiron (47 Kel’Thuzad). Checking in-game, I still have the achievements for the kill, Naxx completion, and 100-club (on 25 only, I may have only gotten that one recently). Some of my alts have missing kills that seem odd too, but I can’t remember for sure if I did them or not.
I’m pretty sure this is new, as a few months ago, I went back to start filling in missing raid kills (mostly from WoD onwards), and didn’t notice any gaps on earlier raids.