If they had heard Hayne call for a fair catch, the 49ers' special teams unit would have peeled off and let Hayne have space to take a fair catch and kill the play.
"You just have to make a decision earlier," McGaughey said.
"You can't wait that late to throw a fair catch up in traffic like that.
"Again, that comes with time and experience and is kind of hard to simulate in practice."
49er LJ McCray crashed backwards into Hayne, who fumbled the ball.
Hayne, who has only played eight American football games in his life after quitting the NRL, also fumbled a catch in his first regular season game against the Minnesota Vikings.
McGaughey said despite Hayne's nine stellar years as an elite NRL player, the NFL is different.
"The skill-set might be similar, but it's two totally different games," he said.
"Two totally different strategies.
"They are worlds apart literally.
"But, every situation is a learning situation for Jarryd because he has never played football before."
The 49ers, after three straight losses, face another tough test on Sunday when they travel to the New York Giants.
In an Australian-on-Australian battle, Hayne will field punts from the Giants' Aussie rules-raised Victorian Brad Wing, who has been in top form.
-AAP