I just re-see the beginning of the season ....and there's two things i always found weird...
When Ben is apparently trying to kill her and Jack in the epi 1 she seemed surprised, apparently she believes he really wanted to kill her... and then jack told her "he seemed happy to let you die" It hurts her and when jack continue saying is the one in charge, he's the one who's making decisions, she answers: "we make decisions together i don't answer to him"
And later before the operation she said to Jack that this is gonna sound weird but "i've always been very good at following orders" if she's lying i don't get why? so i'm assuming she's telling the truth!

So maybe she's not following Ben's orders but orders from someone else???Jacob (who could possibly work for the hanso foundation or someone like that)?Richard?
Maybe she sent the losties in a trap and she perfectly knew it that's why she came back...:rolleyes: :confused: :confused: