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In Episode 472 of Naruto Shippuden, Kaguya and Black Zetsu thought Naruto with Truth Seeking Orbs surrounding was the original among the clones, but it turned out to be a clone once Kaguya struck him with one of her black Rods.

Why couldn't Kaguya use her Byakugan to see the original Naruto? Byakugan can see the real ones among clones and I don't think anyone has a stronger Byakugan than Kaguya, right?

And if Naruto had Nature Energy and couldn't be seen- so does Kaguya, she can merge into nature and kill enemies by merging into nature as per Epsiode 470, when she teleports everyone into Ice World and turns into Nature Energy and traps Naruto under icicles.

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This is because the Byakugan can't distinguish the clones from the original when a jutsu like Shadow Clone is used. Had it been the basic Clone Justu, then she would have easily been able to distinguish the clone from the original.

The Byakugan can see chakra to a greater degree than the Sharingan. This enables users to distinguish certain types of clones from their original and even identify specific individuals' chakra signatures

Source, empasis my own

Neji states during the Chunnin exams that the Byakugan is not able to distinguish the real one amongst the shadow clones due to 1) the chakra signature is the same and 2) the charka is evenly distributed through the caster and the clones

Naruto, Chapter 11

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    and I also remember Neji having a hard time distinguishing White Zetsu clones. Mar 4 at 6:51

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