The Barcelona superkid joined up with the Spain squad before being released after the RFEF were informed Yamal needed 10-12 days rest after an injury examination was held on the Sunday.
The RFEF insist Barca did not inform them of Yamal's medical procedure until after he had joined up with the La Roja squad.
Asked about the controversy, Llorente said: "I don't have any problem with him. The problem is with the Federation with Yamal. These are things that can happen in football.
"In the end there is a lot of load of games, the club sweeps for its home and the Federation for its own. It is understandable that there is friction because everyone wants the best for themselves and he is a very important player.
"It is clear that there are many games, many trips, that the body takes as far as it goes, but as the Rayo coach (Iñigo Pérez) said, whoever wants to get out, let him get out of this wheel. It's screwed, there are a lot of games, it's too much, but you have to be working, trying to make all those things influence as little as possible, be healthy and that's what it is. Whoever wants to leave, let him go. It is clear that we have to fight, but we have been doing it a lot and nothing changes."
Llorente added, "I didn't have the opportunity to talk to him, I imagine that it will not be a dish of good taste to experience these types of situations. Being a young player what he wants is to play football. I wish I didn't have that discomfort and everything could be normal, but these are difficult times that I imagine he will cover with his family."