You're not up to date on the latest trade literature, I see. There are plenty of instances where free trade can hurt a country. Smith did not forsee the infant industries argument, for example, that's been around for some time. The case for free trade also breaks down when you're dealing with industries where there are large economies of scale, especially if these industries lend themselves to natural global oligopolies. This is again something Smith did not forsee because there were no such industries in his day and age. There are plenty of other examples.
Smith was a brilliant man, but his ideas are dated. He was writing before the advent of the industrial revolution, for crying out loud.