I think everyone else has jumped to the most obvious conclusion, which is most likely wrong. Most Japanese factory exhaust systems have dual wall pipes on the headers to keep the pipes from getting hot and discoloring the chrome, turning it blue or gold. Many other manufactuers use singlewall pipe, even the expensive ones. Look at any BMW, old Norton or Triumph and many Harleys and you'll see the discoloration. Most aftermarket exhaust systems are singlewall as well, which is how they get more flow capacity with the same outside diamater pipe.
Since you have a complete Yoshimura exhaust, I expect that's the cause...single wall pipes. If the bike runs well, doesn't stagger, stumble, knock or ping and seems to have adequate power delivery without flat spots, then I wouldn't worry. Now if the Yoshi system does have double wall header pipes, them take the advice of the others.