The balance of the Ferrari wasn't right, Max Verstappen set the pace for Red Bull and Vettel brushed the wall at the end of practice one then sat out the first 34 minutes of the second session while waiting for the auto to be repaired.
Cue some serious work overnight, both in Montreal and at Ferrari's Maranello base with reserve driver Antonio Giovinazzi putting in the miles in the simulator.
But asked whether he was beginning to have any doubts about whether Mercedes' W09 auto was capable of taking him to another world title, Hamilton said: "I don't let that get into my mind".
Valtteri Bottas says the Canadian Grand Prix shows Mercedes needs its engine update as soon as possible after being unable to challenge Sebastian Vettel. "All round they've been doing a slightly better job so we've got to do more". I still think we're not pretty good in Monaco and Singapore.
"I was just really happy to finish", said Hamilton. "I could have lost a lot more today".
Daniel Ricciardo, a victor two weeks ago in Monaco in another race panned for being tiresome, brought his Red Bull in third, just ahead of defending champion Lewis Hamilton's Mercedes. With 20 laps remaining, Hamilton began to find a rhythm to move within a second of Ricciardo while Bottas, at the front, trimmed Vettel's lead to 3.8 seconds. "I'm just grateful the engine made it". And a miscalculation that saw a race official waive the checkered flag when there was still one lap to go.More news: Doug Ford's Progressive Conservatives win majority government
It was left to Bottas to chase Vettel, who made a clean getaway from the start, with Verstappen nearly passing the Finn before the order settled down.
Mercedes brought just five sets of the hypersoft per driver to Montreal, while rivals Red Bull and Ferrari had eight.
Given the potential for unpredictability in Formula One and engine reliability likely to become more of a factor come the business end of the season, Hamilton was aware of the importance of getting his auto home to the finish.
New Zealander Hartley had been trying to pass Stroll on the opening lap when the latter had a brief wobble, causing the two to clash. Both cars were badly damaged but the drivers were uninjured.
"I am still here to win, I still believe we can win", Hamilton said.
Here's what else we learned in the Canadian GP.
Fernando Alonso's F1 future remains unclear after he retired from his 300th Grand Prix before making his Le Mans debut this week.