The AFL has defended its tough penalties for teams breaching interchange rules and reminded clubs that things could be far worse under the old system.

St Kilda and the Brisbane Lions were both penalised over the weekend after players crossed the interchange line before teammates had completely left the field of play.

Under the controversial new rules, the Saints and Lions both had to watch as the ball was returned to the centre for their respective oppositions to be awarded a free kick and 50-metre penalty.

St Kilda lost the lead in the final quarter on the Gold Coast last Saturday night as North Melbourne kicked a goal from Luke Ball overstepping too quickly, although the Saints regained the lead and won the game.

But the Lions' indiscretion, paid in the second quarter at the MCG on Sunday when Luke Power was too quick off the mark, was ultimately costly.

The resultant behind equalled Melbourne's winning margin.

But AFL football operations general manager Adrian Anderson, who saw both incidents, denied that the punishments were too stiff for the crimes.

Anderson said the penalties - introduced after round six, when Sydney briefly fielded 19 men in the drawn match against North - were acceptable compared to the "Draconian" previous rule, where sides could be stripped of their score if a head-count showed they had too many players on the field.

"A free kick and 50 (metres) or from the centre square plus 50 is a penalty that is a hell of a lot less than losing the entire score that you had for the game," he said.

"It is a fundamental that you have 18 against 18 at any particular time.

"You compare what the situation has been, you could have the score go back to zero.

"That is a Draconian penalty by comparison with 50 metres from the centre of the ground or 50 metres from where the ball is.

"I think you saw from Sunday's game is that it's not a guaranteed goal as well - you can miss - and it's always been a fundamental that there must be 18 against 18.

"We've made that very clear, we've made the process more streamlined so it should be easier for the clubs to (work)."

Lions coach Leigh Matthews acknowledged Power's mistake had caused the infringement, but said the penalty could be considered too tough.

"We know the penalty, whether the penalty's too severe for the events, I guess that's an interesting judgement," he said.

"It's a pretty severe penalty for a minor offence, but the idea is there's only supposed to be 18 players on the field at any one time. That's the rule, anyway, and we all know the rule."

Matthews said the incident had no impact on play and felt the Lions might have been more hard done by another controversial ruling.

Melbourne were awarded another 50-metre penalty, in the final quarter, when Lions physiotherapist Nathan Carloss ran across the mark, giving Demon Lynden Dunn a shot at goal. He also missed.

Matthews said Carloss was "very unlucky", as he tried to get out of the way.

He said he would consider calling umpires boss Jeff Gieschen for a clarification on the rule.

"I might just ask the question, is that right or was he just unlucky (or) was the umpire a bit overzealous?" he said.

"But the only reason I ever ring the umpiring people is for interpretation clarification.

"The decisions will be made, some of them will be wrong."

Meanwhile, the AFL is yet to consider calls this season from Richmond coach Terry Wallace and Collingwood counterpart Mick Malthouse on expanding the interchange bench to cover for players who suffer game-ending injuries.

Anderson said clubs had the right to lodge submissions advocating rule changes to the laws of the game committee.

"There's no point me hypothesising what might or might not happen," he said.

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