Dust happens. The LCD is not pressed up against the glass in these phones (or any that I can think of?). There's always some gap, there's always a path INTO the phone, and so there will always be a chance of dust entering the phone. I have a fair amount of dust in my 1yr old 3GS. The dust doesn't hurt anything, just might attract your eyes if you're really worried about it :).
If it REALLY bugs you, you can remove the display assembly and try blasting the edges with compressed air to try to push the dust out. I would not recommend trying to separate the glass and LCD. It's going to cause more headaches then solutions by a ration of approx. 1:125498423456123 with an uncertainty of .01%. Point being, if the Apple store won't replace it (I cant imagine why they would, it's not broken), I wouldnt bother with it.
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