In my case it concerns the skyshard in "Bad Man’s Hallows" (In the roots of the Hallows).
My achievements list says I don't have it, but I'm pretty sure (nowhere near 100% though) I've picked that shard up.
But if I did not it doesn't show up in the dungeon at this moment.
My shard count is 1/3 which would indicate I have picked up every shard so far; 3 from Betnikh, 3 from Stros M'Kai and 16 from Glenumbra (22 devided by 3 leaves one).
So either the shard is missing in the dungeon or the achievement list is wrong ...?