Well yes, it makes no sense if Desmond is an "exception" in the sense that he can create alternate timelines. The writers can't have it both ways. Either there's only one timeline or there isn't.
But there's no logical contradiction if, as I suggested earlier, Desmond is only "special" in the sense that his memory is swiss cheesed.
Correct, there's no logical contradiction in that case. I was thinking of Desmond as the special one who could change the past. Or future, as the above poster points out, which is not a physically meaningful distinction.
Given the long term use of flashbacks, though, wouldn't calling their validity (if for one character, why not all?) into question sort of undermine the whole series?