The incident in question saw players given the thumbs-up to return to the field prematurely.
Fox Sports revealed the players were let back onto the park after eight minutes and 19 seconds of their 10-minute bin.
Api Koroisau and Dylan Walker were in the bin as the controversy unfolded, but Walker didn't take the field due to a head injury assessment.
Koroisau and Matthew Wright were allowed to return to the field.
"This is a monumental stuff-up," a livid Andrew Voss said on Fox Sports. "There's no other way to explain it. The NRL has to take responsibility."
The NRL claimed it was the responsibility of each club to elect someone to keep time.
NRL legend Greg Alexander put the blame on the competition and not the club.
"The NRL owns the sideline. They own the clock and they own everything that happens on the sideline," Alexander said.
Scott sent off in NRL drama
Curtis Scott was sent from the field after giving Dylan Walker a shiner midway through the second half as the two sides squabbled in a low-scoring slugfest in Melbourne.
The blue that followed had fans up in arms after the referee sent Walker, who was the first to cop a punch, to the bin alongside Api Koroisau.
Akuila Uate stopped the Storm from scoring late in the piece with a stunning try-saving tackle to stop Will Chambers on the right flank.
Manly broke through with a late try set up by Daly Cherry-Evans with 11 minutes on the clock. A precise grubber from the skipper sent Tom Trbojevic over the line under the posts and set up an easy conversion to bring the score to 16-4.
Controversy explodes in thrilling scenes
The Cowboys looked buried by the 60-minute mark but another penalty granted to the home side left skipper Johnathan Thurston an opportunity to close the gap.
A second try to Antonio Winterstien and a magical conversion by Thurston levelled the score in the final 10 minutes.
Michael Morgan found space to squeeze a field goal in the 76th minute and looked to have the game wrapped up, but a break up the field with under 40 seconds left in the match sparked hope in the Rabbitohs' sheds.
A botched field goal attempt from Adam Reynolds had the Cowboys celebrating, but a whistle blown against Jake Granville for rushing in too early after the tackle gave Reynolds an easy penalty kick to finish the game 20-19.
Granville was spotted tearing up after his game-changing blunder cost the struggling Cowboys another home win.