The holes in the towers
Neither of the holes in the WTC towers could have been made by an airliner that penetrated the building completely. There are huge obstructions in place that would make it impossible to get an airliner through either hole, even in bits. For a fragile aluminium plane to have gone through those holes without exploding on the outside or shedding bits on the outside is totally impossible. And a fragile aluminuim plane could never make a cookie-cutter type hole in the huge steel that the WTC outer walls were made from. That only happens in cartoons.
The way these holes were made is at present undetermined.