Shisui Uchiha has 2 eyes, Danzo took one while Itachi was gifted the other. As with every mangekyuo, each eye had a different ability. What you’re referring to isn’t Kotoamatsukami, which was the ability of the eye Itachi has, but the Doryuoko, which was the eye that was ableClones and FTG are counter for both Kotoamatsukami and finger genjutsu.
As we know from manga person who is sensor can sense change in chakra flow and tell if someone is under genjutsu . If Tobirama is caught inside finger genjutsu his clone will sense it and immediately teleport original to himself and release him.
Same goes for Kotoamatsukami , Itachi only has one shot pre 10 years and based on feats Koto can only be used on 1 person (Danzo wasn't able to use it on both Sasuke or Tobi). While person caugh inside Koto can't realise that ,we know based on feats that other person can as we saw with Ao. So again clone will sense change in chakra flow and teleport and release original ( assuming Itachi actually traps original and not clone)
to control people without them noticing I.e danzos eye