Stuart spoke to the media following the game and says there's a discrepancy between what's penalised for the Eels, and against them.
"I've got no argument with the fact we get penalised, most of them are deserved. But the same actions aren't being penalised with the opposition team," he said.
"The opposition isn't copping the same as we're copping."
Stuart says assistant coach Dean Pay deals directly with referees' boss Daniel Anderson, but isn't seeing any changes.
"All we've done is tried to train with discipline; I've tried to get the boys to live with discipline, we've worked that hard with discipline off the field."
"But we can not be so different every week from the opposition - not with penalty counts, but what we're penalised for."
Ricky insisted he was not being a sore loser by pointing out problems with the referees, adding the Rabbitohs side deserved to win.
"That roster is marvellous - they're a good footy team," he said.
"I said at the start of the year and there's not any reason why I should take it back - they're a fabulous footy team and can win the comp."
Despite the loss, Ricky says the effort from the Eels players was strong.
"They tried really hard for 80 minutes this week, which was really good, I was pleased."
Watch the highlights from the game here.