Well, when Naruto was fighting Sasuke at the Valley of the End, Sasuke popped a hole in his shoulder, to prevent him from using the Rasengan.
Naruto, in response, activated his Nine-tails chakra (to less than one tail), and the hole healed so fast it was actually visibly closed.
A few years into the future, Naruto has (almost) complete control over the Nine-tails' chakra! And yet, when he attacked Kisame, he twisted his ankle, and that didn't heal until much later.
What the hell? That chakra had enough life force to sprout trees from Yamato's logs! Why couldn't it heal a simple twisted ankle? Can we dismiss it as a case of "Allow Gai to fight Kisame and provide Naruto an excuse to stay out of it"?