Yeah, there is always the real/original/true Naruto mixed in somewhere. In his fight with Zabuza he smothered Zabuza with shadow clones and used them as a distraction to cover the fact that he was transforming into a shuriken as is explained here. In his fight with Neji during the chuunin exam Neji actually destroys Naruto's shadow clones and leaves him the last one standing or not more than once. In that same fight when Naruto uses a large number of shadow clones Neji ignores all of them and attempts to attack the real Naruto because doing so would dispel the jutsu. I can think of a few more examples. I'll just use the two examples I can think of at the moment that best answer your question. When Naruto and Kakashi were fighting Deidara and the kyuubi cloak came out and Naruto went two-tailed all his clones were destroyed, this also happened when he was developing the rasenshuriken. The best example I can think of now though was when Naruto and Sakura were having their training battle against Kakashi, Naruto used a shadow in midair in order to pull his real body out of the way of Kakashi's shuriken, here.