The Portuguese says games against fellow top six teams have shown weaknesses in Frank Lampard's young side.
But Merson told Sky Sports: "I think that's a bit harsh, Mourinho.
“The Man United game at the start of the season, that was never a 4-0 in a month of Sundays, that could have swung either way.
“Ajax are a very good team, very good team. Let's look at the positive, they were 4-1 down and come back and drawn 4-4, probably should have won the game.
"Man United [in the Carabao Cup], he rested players. Man United probably played their best team and Chelsea rested [players], and it took a worldie goal.
“It doesn't matter who you are as a manager, if people go and do something special on a football pitch like [Marcus] Rashford did with a 35-yard free kick when Chelsea were getting on top at the time."