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There seem to be quite a few discrepancies in Danielle's character. Either these are small continuity errors or part of some big 'Danielle' explanation that answers your question. Despite the producers metticulous plotting, much of the issues stem from small glimpses we get at the very early days of Lost. Its only once her story is fleshed out that descrepancies appear. I'd be inclined to believe its mostly covered by Danielle going a bit insane early on. Ben even refers to her as this "crazy women he stole a baby off" just before Alex is shot. Who knows how Danielle coped with losing (killing?) her team and then losing her baby? She described it as having been taken by the others but also having never seen the others. Perhaps she convinced her self that Alex simply disappeared in the night rather than deal with the fact she could maybe have stopped Ben if she had acted?

That said, I reckon we haven't seen the last of Danielle just yet :)