I think one of the biggest problems now is that Mbappe is the one striker that the opponents can focus on. He is the most dangerous weapon that Real Madrid has and when Vinicius Junior and Rodrygo are injured, it makes it quite predictable for the opponents what Real Madrid is about to do. It is sometimes the same for Manchester City when the opponents focus on taking Haaland out of the game. It works out quite often since they know that Haaland is the center of attention for their attacking game.
But now with 2 top stars being out of the game due to injuries, the opponents can't of course neglect the other substitute strikers, but the game will still be centered around Mbappe. They can get him covered man to man and in space. That means he can barely use his speed to create chances for himself and once he has got the ball, he is probably surrounded by at least two players towards the opponent's goal.
Usually with a player like Mbappe you want to play a system with 3 attackers, something like 4-3-3. This makes it very hard for the opponent to guess the next move. Like Barcelona played with Messi, Suarez + one more striker. That's almost impossible to defend for an entire game when you know that all 3 of them have the ability to strike from literally anywhere and you have a player like Suarez who can perfectly cover the center. Mbappe prefers to speed up on the wing and then find his way to the center during the dribbling.