A penalty was called against the Swans when Adam Goodes came off the ground and Dan Hannebery entered the field of play at the 21-minute mark of the third quarter.
Confusion reigned as the Swans protested their innocence and said they still had the maximum four interchange players on the bench as an umpire awarded a free kick and 50m penalty to Carlton's Setanta O'hAilpin.
O'hAilpin kicked a goal to put the Blues seven points up. They held on to the lead and booted four goals in the final term to eventually win by 16 points.
An AFL spokesman confirmed after the match that the decision behind the free kick would be investigated throughout the week.
Swans coach John Longmire was furious about the free kick when he spoke to the media after the game.
"My first thought was that we had plenty of players on the bench and not enough players on the ground," he said.
"I could see that from the coaches' box. So I'd have to go back and check Champion Data and the vision, but from my own eyes about 80m away sitting in the coaches box, I thought we had plenty of players on the bench."
Longmire said if the decision was found to be wrong, officials had to be held to account.
"If that was a mistake and it's a pretty basic one, not a difficult one, do we just move on and say 'Oh well, that was a mistake'?
"I think there's got to be some pretty serious consequences to it if it's proven."
Longmire said there was no reason that the decision couldn't be reversed and that there would be very little added to what was already a lengthy hold-up in all the confusion.
"There seemed to be a fair delay where if there was a mistake it could have been rectified straight away. I would have thought there was a bit of time to do it," he said.
"If you looked around and counted the numbers on the bench there might've been time to do that. I might issue my own 'Please explain'. Maybe I'll do that."
Longmire said he disputed one suggestion from officials that the confusion came from the Swans having too many interchange players.
"One of the guys told us we had five on the bench. I don't think there's a penalty for having five on the bench. I'd be pretty dirty on ourselves if we had five on the bench," he said.
"We're wired up to the interchange box. All our people were telling us we had plenty of numbers on the interchange bench. The people who were watching the interchange bench told us the same thing."
