Am I the only one that thinks that back in Chapter 366 that there was more to the conversation between Naruto and Itachi than we saw. Maybe Itachi didn't just do something to Sasuke but to Naruto as well (which would partly explain him being injured prior to the fight with Sasuke). If Itachi really did want to protect his brother I doubt that the only thing he did before he died was give Sasuke amaterasu.

Not only that it's perfectly possible that Naruto doesn't even know something was done/given/said to him, Itachi could of just trapped him in a genjutsu (since we all know how hopeless Naruto is) and done/given/said something to Naruto that is going to be triggered at a latter date (simmilar to how amaterasu is triggered).

If Itachi did do something to Naruto or perhaps gave him something (at the point I'm thinking if he did give something to him it will probably be sealed within him, because lets face it at this point Naruto is little more than a good place to store something powerful) then it could explain why he was hurt at the start of the fight since sealing/transferal techniques ussually take more effort/have serious side effects in the Narutoverse.