Right after John falls down on his side after being shot at from the FBI in the helipcopter on the roof, he yells at them, "I'm on your side you...!!" if you look at his right foot real fast, you will see some sort of foot protection thing.
They actually made several pairs of rubber feet "shoes" for Bruce Willis to walk around in since he was barefoot most of the movie. They just did a bad job of hiding it in that scene.