To explain a bit more about how Naruto is able to pick up on Kakashi's mood, Naruto later picks up the ability to sense negative emotions. The reason he is able to do this is tied to the Kyuubi, and it's Chakra. I've figured that Naruto always could feel said negative emotions but at the moment isn't very skilled at reading theme so it takes him a few days to be able to under stand what he is picking up unless it is incredibly blatant.