Logan Morris's goal after the siren was disallowed after it was ruled he had played on, even though the Brisbane player kicked over the mark.
And during the Showdown between Adelaide and the Power, the ball clearly crossed the line for a behind to the Crows but play was allowed to continue despite the availability of the ARC's video technology.
"Logan Morris was pretty upset, I guess, post-game because he felt like he'd done everything right," Fagan, the two-time Lions premiership coach, told AFL360.
"As it turned out, he had, and I thought that, at that time."
Fagan wondered aloud whether technology was available to check if a player had gone off his line when taking a set shot at goal - or whether players should be told not to try to kick around their bodies in such situations.
"I'd like to think that situation could be avoided in the future. I mean, can you imagine what we would have been like after the game if we had lost by a couple of points?" Fagan said.
"It wasn't a good thing for the game."
The issue has been in the spotlight since Hawthorn forward Nick Watson was denied a goal after the siren a few weeks ago, also for running off his line as he took the kick, even though it made the angle to goal more difficult.
Hawks coach Mitchell has said repeatedly that Watson's goal should have been allowed.
"You can tell if a player is being sneaky," Mitchell said.
"I just think it's common sense. If the player is clearly trying to cheat for distance or angle - play on.
"If he's just having a shot and it's normal routine and he's vaguely in line - I think the man on the mark can actually stand anywhere on the 'plane', not exactly on the spot. So that makes it even more complicated.
"Common sense ... is how I would like it adjudicated."
Likewise, Fagan said there should have been a correction when the ball crossed the line for what was clearly a behind to Adelaide's Riley Thilthorpe in the last quarter of Saturday night's Showdown.
Instead, play was allowed to continue and the Crows' Ben Keays goaled from a free kick paid seconds later, though on this occasion it didn't influence the result as Port Adelaide scored a 26-point win.
Fagan was asked if the game was tripping itself up because the enforcement of the rules was becoming too complicated.
"It seems to be it's the case with humanity - we've just become more complex, the longer we've existed as a civilisation," Fagan said.
"Common sense isn't all that common. Somewhere, there needs to be somebody who is looking closely at common sense at AFL House, bringing that to the game as much as possible."
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