The Rabbitohs could be fined up to $10,000 after 14 players were seen to be on the field in the 27th minute in the rush to replace an injured Sam Burgess.
An NRL sideline official had accepted cards for each of the changes but the responsibility for having the full team of 13 men falls to the team manager ultimately.
Souths' Coach John Lang admitted a mistake had occurred but was not sure how it came about.
A breach notice may be issued to the club today.