France star Mendy was reported to have been at the Manchester nightspot until 0230 GMT, according to British media on Tuesday.
Mendy had not been included in City's squad for their Premier League win at Fulham later on Saturday.
Instead, he was due to attend a training session as he battles to return to fitness following another injury-plagued season.
City boss Guardiola admitted he couldn't force Mendy to stay at home, but he made it clear he was frustrated by the player's latest high-spirited incident.
"They are old enough to know what they have to do, I'm not his father. I would prefer him to go home earlier but I don't control the players in that situation," Guardiola told reporters on Tuesday.
"(I'm) not frustrated, I'm a relaxed guy. It might not look like it but I sleep quite well."
Mendy, 24, has had two injury-ravaged campaigns at City since joining the club in 2017.
He has appeared only once for the English champions, as a substitute in the League Cup at Burton in January, since undergoing meniscus surgery in November.
Mendy missed most of his first season at the club with a cruciate ligament injury.
He was also the subject of disciplinary action last September when he reported late for treatment on a foot injury having attended a high-profile Anthony Joshua boxing fight in London the previous evening.
Guardiola said Mendy is now fit and in contention for Wednesday's clash with Cardiff at the Etihad Stadium.