The Cats beat Collingwood by 25 points on Thursday night but the free kick count was 24-7 the Magpies' way, leaving Scott bemused.
"I wouldn't focus too much on the 24 part, but the seven part is very strange," Scott said.
"We've had a few games like that this year.
"If it's 7-12 it's a 'put the whistle away' kind of night, but there's a few things that I would describe as strange at the moment.
"I think we've been here before, haven't we? It's not the forum to be discussing these things but that's not to say it shouldn't be discussed."
Scott had no plans of taking his concerns up the chain at the AFL .
"The confusing parts arise when you think you understand the rules really well, explain it in great detail to the players and then you don't see it play out that way," Scott said.
"That's the part that we need to straighten out, that's really our only role.
"I think at some point it's good for the people in charge at the AFL to consult broadly, especially the people that understand the game really well, which tend to be the coaches.
"… We'll get consulted at some point, give our input."
Scott said he only addressed how games were being adjudicated with his players when he noticed a "shift" in interpretations.
"They deny it, but there's definitely been a shift in holding in the marking contest," Scott said.
"It's really important you adjust with that - double down on the cues, what they're looking for, are you giving them a reason to pay these free kicks?
"... I will bring up one issue that is confusing for everyone, when you have an umpire 12 metres away with a perfect view and he gets overruled, that's strange."
Geelong had tagger Oisin Mullin go to Collingwood superstar Nick Daicos to limit his impact.
When asked how close to the edge Mullin went in terms of his physicality and blocking when tagging, Scott said: "Probably pretty close.
"But it's an interesting part of our game, isn't it? Because holding in the marking contest should be the same as a ruck contest which should be the same as a ground level contest.
"I think we all know that intuitively that's probably not the way it's interpreted.
"... I push back on the people that say 'there's a rule of the week and the umpires have changed'. They should change, exactly the same way that we change.
"The difficult part for them is that if we have concentrated on something, do we communicate it? Because if they communicate it, they get criticised for that as well."
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