Naruto can sense evil and hatred (and maybe other feelings) while in Kyubi Mode. When he was originally training with Bee and sensed that something was going on outside, he insisted on going outside. This was in a place that was supposed to prevent him from sensing things that were outside the cave and outside the extremely powerful barrier.
Naruto also could sense where the other Jinchuriki were after the light flash attack that was supposed to blind him. This is also why he can tell the difference between the Zetsu clones and the real people. Zetsu is supposed to be able to make exact copies, down to the chakra that are completely indistinguishable from the original.
