During the first hulk-out, as always, the metamorphosis tears through David's shoes, and the Creature is barefoot. Yet when he transforms back into David in the alley, David is wearing shoes, as though he'd never lost them.
When the Hulk is running through Times Square, you can tell that he's wearing sneakers that have been colored green instead of actually being barefoot. (You can even see the regular colored, non-green soles of the sneakers in a few spots.)
When the Hulk runs throughout Times Square, it is obvious that the people are almost oblivious to him. The screams are dubbed in over people carrying on their business, as when the Hulk runs in front of a crowd of people crossing the street.