I'd have to watch the scene again, it could be he notes the souls entering in, but it is there where the souls enter the soulstone.
Which is permanently destroyed - the soulstone or the soul? I think these are kind of questions that most often lore crafters leave open for interpretation - so people ask questions.
I don't really know the D2 lore too well, but there might be something stated some where...maybe even a book haha.
Well of course it would raise questions. If I remember right there were a set of in-game books (audio tapes if you would) that went into more detail on how she tracked down the souls and tagged them. I'd have to check when I get home.
Outside of it telling us what she did, I think getting into specific of how she did it (ie which spell) is getting into specifics only the writers may know. And since it was two different creative teams, of course continunity would be compromised.
I don't mean which exact spell she used, but more like.
-How was she able to track them down, especially the 3 prime evils in hell (that according to tyrael would destroy the souls when the stone is shattered on the anvil)?
-How did she tag them, and get them to enter the stone upon appearance, since the 2 minor lords of Hell killed in D2 died 20 years ago, and no soulstone was taken from them.
-Did she go alone and tread lightly, as all but 1 of the 5 souls would require her to go through the most dangerous of areas, and a majority of them were not Diablo allied as she is?
-How did wise man deckard cain not know of her doing this being the Horadum he is? And maybe he did, but then why did he not question it and find the truth of it knowing his brotherhood knew of the existance of a black soulstone as Zolton was one of them and talk about it before hand?
Basically as D3 goes it is more like:
She did it, who cares, diablo is reborn. With no real details on the knowledge of this.