Skywarpgold

You can kind of see her elbow extending behind her back here. That is also when you can hear the audible "plink" noise.

And here's a blow up of the QoT taking the stone.

You can definitely see an empty stone clasp, on the far right of the necklace, in one of the closeups of Sansa after the QoT touches the necklace.

I think it's simply because he didn't refill his wine until Tyrion did. There is definitely an audible "plink" in the episode as the QoT drops her hand though...

And actually, there's a HUGE audio clue: As the QoT walks by the main table after touching Sansa's necklace (there's also a quick scene of the necklace WITHOUT one of the gems, you can see the empty gem holder), she drops her hand, and you can hear a "plink" as she drops the gem into something (I think it was the wine bottle itself). It's rather subtle, I had to rewind to listen again. EDIT: Grammar fixes.