Confusion surrounded two incidents involving Helan in the first half of the goalless draw in the npower Championship.
A statement from the PGMOL read: "Both Professional Game Match Officials Limited and The FA are to conduct an investigation into an incident that took place in the Huddersfield Town v Sheffield Wednesday game in the npower Championship on Saturday."
It added: "In the eighth minute of the match Mick Russell, the referee, stopped play when Jeremy Helan was adjudged to have simulated an offence inside the Huddersfield penalty area.
"However, it appears that instead of Helan (number 24) receiving a caution, one was given instead for Michail Antonio (number 7).
"At this point the referee recorded the name and number of Antonio in his notebook and advised the fourth official over the communication system that Antonio, number seven, had been cautioned.
"In the 25th minute Helan was cautioned following a foul challenge. As the referee had not previously recorded his name he did not issue a red card for receiving a second caution in the same game.
"The official has subsequently admitted making a genuine error and PGMOL and the FA need to determine why this arose and what sanction, if any, should be administered to the match officials."