Verstappen suffered an issue with a brand-new hybrid component of his Red Bull-Honda, which left him sidelined through most of Friday's second free practice.
The additional MGU-K element added to Verstappen's pool of components might come back to haunt him later in the 2024 season in the form of grid penalties if he exceeds the allowed allocation.
Verstappen qualified beyond his own expectations in Montreal, setting an identical time to Mercedes polesitter George Russell on a circuit that didn't play to Red Bull's strengths.
But the triple world champion has urged Red Bull to cut out its problems, with little margin for error as rival teams have put the outfit under increased pressure.
"It was a nice qualifying session, but from our side we've had too many issues this weekend," Verstappen said as he addressed the engine issue.
"It shouldn't really happen. We keep a close eye on everything, as we always do, but sometimes you have periods when things don't go well for a while and all these little problems come up.
"We have to try to make sure it doesn't happen anymore. Everyone knows that and you always try to prevent it, but at the moment things are just not going so smoothly.
"Of course, we talk about it in the team and we always try to improve or analyse why certain things happen, but somehow, we can’t really stop it at the moment."
Canada comes off the back of a more difficult Monaco Grand Prix in which Verstappen finished sixth as he and team-mate Sergio Perez struggled with the RB20's performance on kerbs and bumps.
What looked set to be a three-way battle for wins with Ferrari and McLaren is now a four-way dogfight, with Russell's pole underlining Mercedes' recent progress with a tangible result.
"Mercedes has easily been quick this weekend, so second place is actually a good result for me," conceded Verstappen.
"We were exactly equal in Q3, but Mercedes was three tenths faster in Q2. Because of that, I think there was still a lot more in it for Mercedes, they haven't really shown their best lap yet.
"I'm happy that it's Mercedes and not Ferrari, because Ferrari is closer to us in the championship.
"But at the end of the day, we have to concentrate on ourselves and make things happen ourselves, because you can't rely on the competition."
In recent weeks, it has also appeared harder for Red Bull to nail its set-up directions on Friday, with the team massively on the back foot in Imola before turning things around ahead of qualifying.
"Somehow, it is just very difficult to make our car feel very comfortable. It looks like it goes a bit easier at other teams," Verstappen concluded.
While the Dutchman has managed to drive around some of the RB20's handling issues, Sergio Perez suffered another disappointing qualifying session, being eliminated in Q1 as he struggled for rear grip.
