Board Thread:Theories and Speculation/@comment-1783334-20150507053750/@comment-1783334-20150507065611

Again when Itachi saw Shisui his Sharingan had the Mangekyo form meaning he hadn't used Kotoamatsukami on anyone. My guess is he used it on Itachi to make him think Shisui killed himself and went into hiding so Itachi would have the Mangekyo.

Also by the time Shisui apparently committed suicide, Madara was already dead and Kabuto only found Madara's well-hidden corpse because of Black Zetsu.