They've already made quite a few mistakes anyway in this arc. It's not canon and Kishimoto is not working on it.
By now, Itachi is 13, that's how old he was when Shisui died in the manga. He was then accused of killing Shisui not too much later and not long after he carried out his MS mission. In the anime according to the last episode, he should be 13 and captain by now. Kakashi should leave by next episode or soon, and if he does not then it is most likely just another mistake on the anime team's part.