Could this be what happened?

[Your Creepy Stalker]

So, a bunch of stuff happened this chapter, Not wanting to spoil it much, But naruto get's disintegrated.

Somehow, this got people wondering how the clones didn't vanish.


When Kaguya warped, Obito, Sakura and Clone Naruto warped to Kaguya's dimention with Kamui.
Sakura gives Obito and the Clone chakra so that the clone doesn't vanish.
Sakura and Obito immediately warped to Kamui World.
Clone poses as real Naruto. Kaguya assumes that the other two were Clones, rather than Sakura and Obito.
Kaguya kills the clone, Real naruto is still in Ice world.
Obito and Sakura warp back from Kamui world to Kaguya's world.

 

[Gagster]

It's simple, Naruto placed Kaguya and BZ under a genjutsu.

 

[Tobi98]

Naruto transformed into Kakashi...

 

[bibspark]

BZ confirmed only 2 got excluding the naruto facing them.
Obito thanks naruto for them hiding in Kumai dimension meaning, the real naruto never entered into that dimension, only the clone, Sukura and obito and the clone creating a diversion for obito to warp to kumai dimension

 

[Ekush]

It's simple, Naruto placed Kaguya and BZ under a genjutsu.

Naah I can't rely on that... Naruto placing someone on Genjutsu is just not possible :// It was surely a clone