Im starting to think Claire died in the cabin when the Merc blew it up.
THen she came back much like Sayid and stumbles out only to dissappear.
That is why the others knew he was "infected". The waters may be some form of healing via Jacob, which didnt work since he was dead (Which is why thewater was colored) and the Man in Black/FLocke can bring people back from the dead with his power, but you become one of his people.
I imagine they dipped young ben in that same healing water.
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