WowAce

Here's a picture.

As you can see it says I got it twice.

It also plays the achievement thing twice.

Unless the AOE looting issue was fixed, which I doubt, that should explain why Skyshards tracking is broken.

Source: https://us.battle.net/forums/en/wow/topic/20747794934?page=1

The very first comment (by Allara) even mentions Skyshards explicitly as being affected by this.

Oh, I see.  When I saw the thing about AOE looting I was thinking it was some kind of toy or something.  I see what you mean now.

 Well, you probably shouldn't have gotten the Found alert twice, but this is not something I can debug (both because I only have a Starter Edition account now, and because farming a Skyshard is way too time consuming). Found Alerts for this item were working for years and I see no reason for that to have changed. The AOE loot problem just means Rarity can't detect all your attempts. Closing this as too much effort to reproduce.