The league last season followed the Premier League in allowing clubs to name seven potential replacements, a system that Hughton believes should have stayed in place.
“I am very disappointed and it is something which has crept up on us,” Hughton told Sky Sports News.
“Seven benefits you. It is a great opportunity for young players to be involved in the first team.
“The worst thing a manager can do is leave players in the stands.”
Teams will still be permitted seven named substitutes in the Carling Cup and FA Cup, but only five in the Johnstone's Paint Trophy.