Board Thread:Episode Discussions/@comment-1181222-20170823100207/@comment-35622277-20170827000901

Maybe it's not that Naruto has to consciously harden his cloak to prevent weapons/attacks from harming him or Sasuke's sword cutting through his cloak, but he instead needs to selectively let things pass through his cloak. He excludes Sasuke and his sword from the list of things he needs the cloak to block, thus allowing them to bypass through.

Think about how Shin's weapons impacted Naruto's cloak, and was lodged there for the remainder of the time it was up. Sasuke and his sword (a weapon) were able to pass through with no difficulties. This probably needs an immense amount of concentration though, explaining why his cloak had dropped when he was impaled.

TL;DR: It's possible Naruto needs to selectively exclude objects in order for them to bypass his cloaks' defenses, while preventing everything else from entering. Because of this, his cloak was unable to block his sword.