That crow already came out of naruto and Itachi killed it with amaterasu ...itachi put a jutsu on that crow that whenever it sees itachi's eyes it will come out, he was sure that after his death sasuke will take his eyes and attack konoha so whenever the crow will come out it will cast kotoamatsukami on sasuke and will stop him from attacking konoha ...but before seeing sasuke, naruto saw itachi so the crow came out and used kotoamatsukami on itachi thus itachi was able 2 get out of kabuto's control ...after that he used amaterasu on the crow coz that eye can only be used in once a decade