The 27-year-old player was photographed at the entrance of a nightclub in Paris, and on a bicycle while in Switzerland.
Some fans claimed the matter was a deliberate snub to Mourinho, who had said just days earlier that players should avoid skiing and cycling to prevent the risk of injury.
Mourinho said in his press conference on the eve of his team's home match against Villarreal in La Liga, "Is this criticism exaggerated? It is ridiculous."
He added, "All the players who were supposed to be here for daily recovery were present. Mbappe came, like the others, to undergo X-rays to diagnose his condition. Then he went to see a specialist in France, because he has a history with his knee that we cannot ignore."
Mourinho, whose team is already six points behind rivals Barcelona in the league title race, countered every criticism directed at Mbappe, as he never shies away from confrontation.
The 63-year-old Portuguese coach told reporters, "Football problems are not enough for you. So you raised the issue of the nightclub, which was not actually a nightclub, as it was used for a private event during Fashion Week."
He continued: "As for the bicycle in Switzerland, it was at a hotel consisting of small houses, which provides them to guests to move around to common areas, and you want to convince us that he was participating in the Tour de Suisse."
Mourinho did not care about the possibility of a hostile reception for Mbappe on Saturday, and reiterated that he is "sure" that the all-time World Cup top scorer has performed "his duties towards Real Madrid".