Fremantle enjoyed a dominant 52-20 inside-50 count in Saturday's win over Brisbane.
But Lyon said a 29-point win showed that his side hadn't taken advantage of its superiority for the second week running, following the round 2 loss to Sydney.
"We wasted opportunities," he said.
"The second half was 30 entries to nine. You should be winning by 60-80 points, not 29.
"It was a continuation of last week's second half (v Sydney), we dominated (inside-50s) 42 to 17 and didn't get enough scoreboard pressure."
Lyon said there was a method issue in Freo's attacking play which the team would be working hard to correct.
"You just can't bludgeon it through the whole time," he said.
"We'll work on that during the week.
"Hopefully we can keep everything else from the last four or five quarters and add to the repertoire."
The coach said he hoped Friday night's match at Etihad Stadium would be played under a closed roof.
"That's going to give you perfect conditions," he said.
"Hopefully, Friday night they shut the roof, there's a big crowd and we get to improve our method and bank four points."
