here's a specific problem, dunno if it's your case

let's talk danzo first: he has 3 kinds of control within his skill set: chaos for 1 round (barrier), chaos for 2 rounds (mystery Y), immobile

all of those will overwrite each other. that means: if unit A suffer from chaos for 2 rounds, but then in that same round suffer from immobile for 1 round, the chaos will be overwritten by the immobile, thus changing the duration of the control.

same as yamato anbu: he has 2 kinds of control: immobile for 2 rounds (mystery), immobile for 1 round (30 combo chase when chakra is above 60)

if unit A is suffering immobile from 2 rounds, and then got hit with yamato's chase at 60 chakra, the immobile for 2 round will be overwritten by the immobile for 1 round, thus changing the duration of the control.

for shisui case, he only has 1 kind of control: chaos for 2 rounds

however, the same thing about overwriting a control can happen if u pair him with a unit who has chaos for 1 round or immobile for 1 round (for example masked man, madara gnw, naruto 6 path, sakura summer, etc...)