Maybe a chronology problem with KA???
Remember Itachi said after one use of KA, you must wait 10years again to actually use the jutsu.
But we all know that Itachi was 13 during the Uchiha massacre which take place just before Shisui died. Shisui said he was about to use KA when Danzo stole his eye meaning he didn't use KA before that moment.
That means if Itachi somehow used KA shortly after Uchiha massacre(what i really doubt. If he used it, who was it against?), the next use of KA would have been at least 10years after(that means when Itachi is 23 at least, supposing he used it when he was 13), which isn't the case.
Remember Itachi even said that the reason why he didn't use KA himself against Sasuke was because he couldn't at that time since the time didn't come at that moment:
So how did the KA managed to be activated during the fight between Naruto, Bee, Itachi and Nagato when it wasn't time for that at all??