The Spaniard reportedly refused to train on Thursday over a club disciplinary process following his red card against Barcelona.
An outburst at the referee against La Liga’s leaders earlier this month saw Costa sent off, then hit with an eight-match ban.
However, the Los Colchoneros boss says the issue has already been sorted out internally – backing the former Chelsea front man to end the season strongly ahead of Saturday’s trip to Eibar.
“What I can tell you is it’s an internal situation, that we solved it yesterday and today Diego was training as he has always trained,” Simeone told reporters on Friday.
“I have explained several times. I do not change what I think about Diego. I think he did not have a good season, marked by injuries.
“And I have no doubt that next season, all the rebellion and all the players who is in all situations that have lived this season, will do very well.
“This season he has not been able to have continuity. Then the expulsion moves him away from the competition from here to the end and all this will make him a rebel.
“Costa will have a hunger and desire to reverse this situation that he has lived this season.
“Players today cannot take anything for granted in the future. Always the players can have the opportunity to leave.
“We always want to compete with the best and those that we consider that can make the team good and keep it growing.”
Asked again about Costa’s punishment over the ban, Simeone added: “I was clear at the start.
“It is an internal issue and has been resolved internally and is now resolved.