Farrell was chasing a kick and Maguire claimed he was pushed into the knee of his own teammate Andrew Everingham by a Storm player as they went up for the kick.
Maguire said Souths deserved a penalty and said it was another moment in the game that didn't go his side's way.
"Dylan Farrell got taken out of play and he ended up knocked out in-goal and the game played on.
"Most games you see players taken out you tend to get a penalty but all of a sudden we end up at the other end of the field so I'll have to have a chat about that.
"The biggest concern is the duty of care of one of our players who was knocked out and the game played on."
Maguire said any time a player went down in that kind of situation, he must be assessed as quickly as possible.
"You've got to look after your players and so does the game."
-AAP