Board Thread:Naruto Discussions/@comment-28939725-20161116235549/@comment-3279282-20161118192122

And his normal Rasengan was drawn blue. And A's raiton chakra was drawn yellow. And Naruto's fox cloak was drawn yellow. And Tsunade's medical chakra was drawn blue. And Mei's yoton chakra was drawn yellow. And Naruto's Rasengan was drawn yellow. And Sasuke's raiton chakra was drawn blue.

Your point?

There's nothing to explain, Naruto's words were a metaphor. He never literally said "my chakra is yellow". His words were "if I had to put it in colours, I would say my chakra is yellow". The manga isn't clear on what colour exactly normal chakra is, but it DOES make clear that Naruto's chakra is not yellow.