Simply put, the plane disintegrated. Aluminum has a melting point of 660C, and fire that resulted from the plane probably produced 1.5 to 2 times that amount of heat for a significant period of time. Furthermore, you are talking about Aluminum, that while a strong metal for its weight, is very mallible and easily malnipulated. The design of the aircraft itself isn't exactly made for head on collision survival. It's designed to survive the pressure changes in the atmosphere as well as the stress of taking off and landing.
You also have to take into account the plane crashes many are used to seeing. They are spread out over a wide area in an open field or even a forest. Very little can be missed in that setting, as anything metal is out of place. Also, there isn't anything to contain the heat produced from a fire. The Pentagon is a perfect structure to contain the sheer amount of heat produced, and contribute to the burn from the materals it is made out of.
This argument of metal melting, or even burning away also applies to the wings. But we must also take into account the wings folding back or crumpling upon impact with the structure of the pentagon. The force of the impact of the wing would be spread out over the entire span of it, unlike the fuselage, which at least as the front of the aircraft to concentrate all the force on, hence you had the penetration that occured.
Look, we are talking about a deflagration/explosion followed by a high intensity fire on metals that easily melt and are mallible. Simply put, the physics alone dictate that few, if any remains of the plane could be found.