Madibo was given a straight red card for the challenge that put Kone in hospital, requiring surgery.
The Qatar defender reportedly went into the dressing room to personally apologise, and Lopetegui hopes the Canadian central midfielder will be able to get back on his feet soon.
Talking to Flashscore as well as assorted reporters, Lopetegui said: "I want to wish all the best to (Ismael) Kone, that he can recover as quickly as possible. This is the main thing, that's why I wish all the best for him.
"It was an accident, what happened. I am sure that Assim did not want to make this injury."
It was always going to be a difficult afternoon for Lopetegui's charges. Playing in front of a partisan crowd inside BC Place, the atmosphere seemed to get the better of Qatar, as they found themselves 3-0 and a player down at the break.
Both of those numbers doubled in the second half, as Canada ran away with the game, and the Qatar manager feels nothing went right for his side in the loss.
He added: "They are a strong team, physically, and they have fast players. They scored very fast, there was one key moment where everything that can go wrong, happened today.
"After we suffer the first goal, it was very difficult. After they shoot three times, they score twice, and they have big quality in the strikers.
"After the red card, it was different. It was a very tough match for us and the players, they did their best. It was very, very difficult to face this match with two players less, in this environment, against this team in a World Cup."
There were two flashpoints in the game, one after the injury to Kone and one at the final whistle, with the benches clearing into a scuffle.
Lopetegui was tight-lipped about what caused it, and would not be drawn as to the reason why his coaches reacted in such a way.
Qatar's next game against Bosnia & Herzegovina a 'final'
The crushing loss means Qatar heads into their final game against Bosnia & Herzegovina needing to win to have any chance of reaching the round of 32.
Both sides have one point from two games, and they meet on June 24th in Seattle in what will be a de facto knockout game.
They will do it without two of their starters. Madibo and Homam Al Amin will both be suspended for the clash after both received straight reds against Canada.
The importance is not lost on the Spanish coach. He explained: "We have to recover the players physically and mentally.
"Today has been tough for all of us, the game before against Switzerland, we made history.
"Now we have one final in front of us, that, despite the tough day today, we won the right to play this match."
Catch up with the game by reading Flashscore's analysis.
Josh Donaldson is a Global Senior Editor and International Football Specialist for Flashscore. From the UK, now living in Prague, Josh specialises in football and cycling and can be found at an obscure ground watching games or on his bike. You can follow Josh on X and read his articles here.
