Not really. I see why people might think that though!
But it could be "where is the punctured tire?", since the "furado" is a quality of the tire in this sentence.
"Where is the tire punctured?" would be something like Onde o pneu está furado? or Onde está o furo do pneu? (which means "where is the tire's hole?"). Then you are asking where the hole is, as opposed to where the defective tire is.