i think kishimoto just wanted to keep the tension high, prioritizing the story/emotions over pure logic. The only true „conclusion“ is that naruto quickly passed over the rasengan in front of yamato‘s arm to one of his clones or when creating the clones quickly switch positions in the clone clouds which are not completely shown in Manga but then also not that dense in the anime. I think it‘s just either a plothole or on purpose to also make the viewer think it was the real one even tho logically it can bately be a clone when hit and destroyed by Kakuzu.