The recently re-signed Perez, whose new two-year deal with Red Bull was announced on Tuesday, followed up his exit in the opening stage of qualifying two weeks ago in Monaco with a similar vein of misfortune at Montreal.
He qualified only 16th in Canada, having been dumped into the drop zone by Alex Albon.
This mirrors a similar run of form last season, when Perez's Saturday performances began to drop off towards the middle of the year - the genesis of which could be traced to the Miami Grand Prix.
Marko reckoned that Perez's woes were purely self-inflicted and that he was uncomfortable in races where track conditions were more critical.
"It's not the car, you can see that with Max. I think it's more psychological," the Austrian said on ServusTV.
"It was close, and when the conditions change, he finds it much more difficult. But the fact that it's already the third time (not in Q3) is painful."
Although Perez looked set to scrape into Q2, he spent the final moments of Q1 teetering on the brink of the drop zone - which he fell into when Albon punched in a lap at the death of the session.
Last year's championship runner-up reckoned that his issues in qualifying stemmed from a lack of comfort with the rear end of his RB20, particularly in the changeable conditions.
He said that this contributed to his struggles to load temperature into the tyres, but was confident that he could enact a fightback to secure points in Sunday's race.
"It was a massive frustration. It was a session where everything reset with the weather. We just couldn't get everything to work, especially the rear axle. I think it was a very strange session for a lot of cars out there," Perez contended.
"We did struggle quite a lot with the rear end, so I think we got to understand what the reason behind it was.
"I think the track being so green it really reset things up but I was struggling to put the temperature into the tyre and I think that was the main struggle.
"We've got some bits to understand tomorrow and we are able to secure a couple of points, that will be a good result and then really just go from there."
Additional reporting by Filip Cleeren and Norman Fischer
