Why wasn't Naruto able to sense Black Zetsu? If Black Zetsu was commanded to be with  Obito while Madara was fighting the 5 kages, 

How come, Naruto was not able to sense Black Zetsu in his Kyuubi mode while fighting with Obito??
One might be able to look at it from the philosophical point of view that there was no evil to sense. 

The rest of this answer may include spoilers


   Black Zetsu is essentially Kaguya's will incarnate. That being said, Kaguya's goals were not inherently evil. Technically, her goal was peace. While it may have been a peace forced upon the entire world, in a manner they did not agree with, in her mind, it was still an act of good. It's true that she did want the power of her chakra back from all those it had been sewn into throughout the centuries. Even still, it is difficult for mere mortals to understand what drives a being that could be consider god-like. Good and Evil being matters of perception, maybe Kaguya truly believed in the good of her actions. Of course, this is all speculation, but one has to wonder, I mean when Kaguya initially thought that Naruto and Sasuke were Hagoromo and Hamura, she wept, so she can't be all bad.

 All that considered, and Black Zetsu being an extension of Kaguya himself, maybe the whole "sensing evil" didn't work because there was no evil intent. But this all hinges on the philosophy of good and evil, and deciding if there is a difference between knowing something is evil and not caring, or not believing something is evil because of the eventual good, it will do.