If I break a rock with a hammer, the hammer stops, but the rock does not get hot. I don't think all the hammer's energy can be found in the momentum of the resulting pieces.
It takes a lot of mechanical energy to produce a small amount of heat, and vice versa. Dropping a ten-pound hammer three feet would, if all of that energy were converted into heat, represent enough heat to increase the temperature of one gram of water by about 10°C. A quick google search suggests that stone has a thermal mass about a fifth that of water. Distributing 100% of the impact energy through 50 grams of stone (concentrating the energy in about 1/10lb) would heat it by about 1°C. I would hardly expect the stone to "get hot" from one such impact. There's just not enough energy there. By contrast, the collapse of the world trade centers represented a release of energy comparable to a small atomic bomb. Even if only a small portion of the energy got converted to heat within the building materials (a lot would get converted into heat in the ground or in the air) that would still represent a really incredibly huge amount of heat. Depending upon how the energy got concentrated, it should not be surprising if parts of the building would get very hot from mechanically-generated heat alone.