Thermite. Which could occure quiet naturally in a building.
Thermite is an incendiary that burns very hot and very fast and requires an initial source that is very hot to ignite it. It cannot be used as a fuel and it doesn't explode. Thermite fails to provide a viable explanation as to how metal of the sort described in the OP could melt as it apparently did.
(Keep in mind that the buildings collapsed in mere seconds.) Now, the metal never necessarily even had to become molten to end up in the state that it did. The fires were hot enough for the metal support beams to act as vicsoplastics. This would have been sufficient to initiate the collapse of floors at the impact sight and those above. The crushing force of those floors as they fell onto floors below them is sufficient for subsequent floors to collapse, resulting in the total collapse of the buildings.
A lot of energy was transferred from the collapsing floors onto those below them and a lot of potential energy was released during the free fall of those floors above onto those below. The energy released by the floors as they collapsed one on top of another had to go somewhere. Much of this kinetic energy would have dissipated to heat and much of it would have caused the further failing of the metal supports (which were never intended to hold up the combined weight of the floors above them, but, rather, to transfer carrying loads from the beams above them to those below them in a chain to the massive footings of the buildings).
The metal twisting and warping as the buildings collapsed would have generated a lot of heat and combined with the heat generated by the buildings' collapse would be sufficient to 'melt' the metal together or deform it such that it would have appeared to have been, at some point, flowing or molten. More likely is that the metal was more squished and deformed because it was considerably softened and put under stresses which would have caused otherwise odd things to happen.
The point is, however, that there is nothing magical, whatever the explanation, required in an explanation of the events surrounding the collapse or the collapse themselves. The case of the metal is not so much a mystery as it is poorly understood.