The France global is out with a foot injury and will miss Saturday's Premier League match against Brighton.
City's manager denied there was any disciplinary problem with Mendy, who has a foot injury, but said: "He arrived late, and that shouldn't happen but it does sometimes".
The report suggests Mendy arrived three hours late for a scheduled treatment session on Sunday, after being seen watching Anthony Joshua's fight with Alexander Povetkin at Wembley on Saturday evening.
Asked if he wanted captain Kompany to be a City player next season, Guardiola said: "Yes. He knows it. I spoke with him", said Guardiola.
On his side's meeting with Brighton this weekend, Guardiola added: 'They have been together a long time, they know what they have to do.
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George and Alex were at Stamford Bridge to see the action! "I'd like to think [I've scored better goals], but probably not.
Mendy received a 12-month driving ban last Friday after accumulating 24 penalty points on his licence for failing to respond to police letters requesting confirmation that he was the driver for four separate speeding offences.
Meanwhile, Guardiola revealed that Kevin De Bruyne is close to returning to training as he continues his recovery from a knee ligament injury.
They also lost 2-0 away to Manchester United in last season's FA Cup, which makes it seven out of eight without scoring away to the big six, and City won to nil (2-0) when they visited the Amex at the start of the season.
"It's incredible. He played the Carabao Cup like it's the final of the Champions League".
The 24-year-old is now suffering from a bruised metatarsal and remains sidelined indefinitely. "I'm not a physio", stressed a visibly unhappy Guardiola.
However, his lateness is understood to have incensed Guardiola and understandably so. 'I think Phil likes to be here, the club has no doubt, the manager has no doubt.