The Argentina international is closing in on a move to Premier League side Manchester City after he arrived in the North West to undergo a medical and agree terms.
The 23-year-old has been the subject of transfer speculation all summer and admitted that he wanted to leave the Vicente Calderon. However, the Atletico coach thinks that the striker could have conducted his move in a better way.
"It does seem that in the coming hours we will arrive at the final outcome of an issue that has occupied us so long," he told Marca. "It is at an end, and I have asked the players to focus on Thursday's game.
"Unfortunately we will not have Kun [Aguero]. The truth is that I hoped to reflect on his decision to leave favourably.
"But I think he could have chosen a more special, professional and loving way to leave."
The Spanish club are reportedly going to receive up to £40m for the forward.