Referee Craig Pawson ruled out Sergio Aguero’s first-half strike at Wembley.
Replays suggested the goal should have stood and City went on to lose the game 2-1 after extra time.
“I think the referees have to stop this,” said Toure.
“I am very disappointed. It is not the first time, there have been a couple of times.
“Maybe on Thursday we are going to have a better referee or maybe play without a referee – I’d prefer that.”
Officials ruled that Leroy Sane’s cross had gone out of play before reaching Aguero.
The Argentina striker later did score to put City ahead but goals from Nacho Monreal and Alexis Sanchez sent Arsenal into May’s FA Cup final, where they will meet Chelsea.
Defeat means City’s focus switches to the Premier League. They are currently fourth but United will leapfrog them if they win on Thursday.
“It is a very big game, an important game,” added Toure.
“We have to do that job and we will see what can happen. We hope we are going to have a good referee.”
