Ok there's some crazy theories going around (like the Others expecting the plane to crash? That's way off) but there really are two possiblities to this completely crazy unbelievable ending to the episode.
1) Naomi is lying, or has been mislead, for some reason or another.
2) The Others, after the plane crahsed, to stop the search for flight 815, faked wreckage.

The reason I hate this second theory is that unlike what people have said you CAN'T just send in footage of a crash, and you CAN'T just dump a plane wreck full of ash and then people will think there's no survivors. If there was not one single body on board that was identifiably in the flight manifest then the authorities are going to know it's a fake.

The way Naomi said it was "They were all dead" as if they found all the bodies but everyone on board was dead .. there is literally no explanation to this. Clones?? No ..