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I've been re-watching Lost (as most of us have) and while watching Greatest Hits, I think I may have an answer as to why Clair didn't get on the Helicopter.
Desmond has said in the past that if he does anything to change what he saw the entire puzzel changes, or something to that effect anyway. Now in Greatest hits he desicribes what he saw to Charlie but no where in this does he mention himself. When he proceeds to go down to The Looking Glass he gets a message from Charlie indicating that the freighter isn't Pennys. This information causes Clair to join Lockes group instead of Jacks, this turn of events could be why Claire didn't get on with Aron.
Now let's all poke holes in my theory :p