Following Argentina's 2-0 group stage win over Mexico in the second round of matches, an unexpected row broke out.
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Canelo sent a threat to Messi when the PSG forward appeared to kick a Mexico shirt that was left on the floor of Argentina's changing room after the game.
The boxer, a proud Mexican, reacted furiously on social media.
He tweeted: "Did you guys see Messi cleaning the floor with our jersey and flag? He better pray to God that I don't find him.
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"Just like I respect Argentina, he has to respect Mexico!
"I'm not talking about the country [as a whole], just about the bulls*** that Messi did."
Canelo, who has 2.2million followers on Twitter, then had a busy 24 hours after the incident, responding to followers as debate raged about the 'disrespect'.
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Sergio Aguero was one of those who replied.
Aguero tweeted: "Mr. Canelo, don't look for excuses or problems, surely you don't know about football and what happens in a dressing room.
"The shirts are always on the floor after the games are over due to sweat and then if you see well, he makes the movement to remove the prize and accidentally hits it."
Canelo then quote tweeted Aguero and hit back: "You too, b******? You used to write me, 'Oh, oh, Canelo', and now you're crying. Don't be a hypocrite, b******."
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A few days later, after some thought, Canelo offered an apology.
"These past few days I was carried away by the passion and love I have for my country," he tweeted.
"I made comments that were out of place so I want to apologise to Messi and the people of Argentina. Everyday we learn something new and this time it was me.
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"I wish both teams much success in their matches today and here we will continue to support Mexico until the end."
Not long later, Mexico were eliminated while Argentina progressed from the group stage.
In the end of course, Messi led his country to World Cup glory and lifted the trophy on Sunday.
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In reaction, Canelo has now tweeted: "Muchas felicidades Argentina, se lo merecían."
This translates to: "Congratulations Argentina, they deserved it."