In the "Pilot, Part 1", Charlie is seen running to the front of the plane to enter the toilet. When the plane hits turbulence he leaves the toilet and takes a seat in the very front of the plane. This is interesting since it would appear he emerged from the middle section.
Charlie was shown sitting down in a seat sporting the same seat cover as the seats Boone and Shannon were sitting on. The seats in First Class look different (tan leather coating), as seen just before the cart almost hits Charlie. This suggests that Charlie made his way back far enough to end up in the middle section.
The Others crashed a fake plane, and used bodies from the front section.
This is unlikely as they all appeared shocked at the plane crashing when we saw it from the perspective of the barracks.
The bodies found in the seats at the bottom of the lake belong to Jeff and Gina.
As seen in Charlie's flashback the first class cabin looks full but when seen in Pilot, Part 1 the first class cabin looks empty, it is full of debris,wreckage and a few dead passengers,also there are seats missing and seats that are empty so that is a clue that there are survivors from that section.
People could have been sucked out of it when it broke off from the fuselage, just like when the tail was broken off of the fuselage.
Is it possible that when we see the monster during Pilot Part 1 it is killing the survivors of the front section? This would explain why we don't see all of them when Jack Kate and Charlie visit the cockpit.
The people who were missing from the front section of the plane were sent some time into the past and formed The Others or joined the Others.