How could Naruto twist his ankle? 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"?
During his battle with Sasuke in the Valley of the End Naruto was not in control of the nine tails. The Nine Tails was acting on his own accord, triggered by the emotions of Naruto.

But during the battle with Kisame, Naruto was in control of the Nine Tails. Infact he had just gained control of it. So I would guess that, since he only recently gained control of the nine tails, he was not in sync with the Nine Tail's power, which is displayed by Naruto misjudging his speed and power thereby spraining/fracturing his ankle. 

One can have all the raw power in him, but unless the body is in sync with the power, you are no good. Also, about the fallen Zetsu's or wood element's sprouting leaves, this is not done by Naruto, but rather it is done by Naruto's/Kurama's chakra resonating in the wood element. (Zetsu has Hashirama's cells).

Well this is my two cents.