Carrasco was replaced by Angel Correa with 18 minutes to go in Azerbaijan and his questionable body language was highlighted by numerous fans and pundits.
The Belgian casually wandered off the pitch with no urgency despite Atletico's need to get a goal and some perceived that as showing a lack of interest.
But Simeone revealed that the attacker has been struggling with a knee complaint and will miss Sunday's trip to Celta, insisting Carrasco's attitude has nothing to do with it.
"He's not going to participate [at Celta]," said Simeone.
"He is making a huge effort, with knee discomfort, to help the team. I am very happy with him, he is decisive in the team, very important for the future.
"We were talking with him a long time ago; we need him well, the group wants him to be strong and hopefully he will recover.
"And the attitude; the players always want to play, to be on the pitch. It's normal that when he leaves he does not show joy."
One player who is nearing a return, however, is Augusto Fernandez, who has been out for over a year after tearing his anterior cruciate ligament in September 2016.
The Argentinian could even make his return against his former club Celta this weekend, though Koke is expected to miss out.
"Koke is still in a bit of pain so he will rest this match," said Simeone. "Augusto is much better.
"He is growing a lot and he a big chance of participating and playing, we need him because he has a great vision of the game.
"He is very excited because it's been a while without playing, with all that enthusiasm and his importance as a player, he will be an important midfielder as soon as I put him in the field.
"He's okay, he's doing much better and he will be there fighting to get a place to play."