He wanted Sasuke to take his eyes so he will have the EMS because he knew a war was coming. His plan was to let Sasuke have his eyes(thus making Sasuke immune to blindness) then when he used his eyes vs Naruto he would then be forced to protect Konoha. Obviously vs Tobi. His plan failed because Tobi knew about Itachi's sacrifice with his clan. Which Itachi never wanted Sasuke to know or else he would seek revenge against Konoha. This is ultimately why he left the crow with Naruto.
The actual question your asking though is very simple. Itachi wasn't in control of his body when he used his MS. Itachi obviously knew he was about to use Ama so he said "lets see what happens" but remember his body wasn't in his control, only his mind. Then the crow popped out and Shisui's eye placed an genjutsu on Itachi breaking the control. It was just luck, and bad luck at the same time.