Speaking on the eve of Wednesday's LaLiga clash at the Wanda Metropolitano, Simeone appeared to call into question the Portugal international's lack of work-rate.
"We are a team, not just one player," he told reporters. "We need everyone's contribution so that the team can function as a team, and that individuals and talent can excel."
Joao Felix has scored two goals in his past 16 games and was dropped to the bench for the 1-1 draw with Real Madrid at the weekend, but he played 67 minutes against Athletic.
However, Simeone insists his remarks were misconstrued as he was talking in a more general manner, rather than about the 21-year-old specifically.
"Either I express myself badly, they interpret me badly or they just do what they want," he said at his post-match news conference.
"I speak of a general will. It is the most important thing in life; without it, the rest does not exist."
Atletico's win over Athletic in their game in hand moved them six points clear of Barcelona at the top of LaLiga and a further two points in front of Real Madrid.
Iker Muniain gave the visitors the lead in the Spanish capital, but Marcos Llorente equalized in first-half stoppage time and Luis Suarez scored a penalty winner in the 51st minute.
It was just Atleti's second win in five matches in all competitions during a patchy spell and Simeone was pleased with the way they responded to a late setback against Madrid, when Karim Benzema equalized in the 88th minute.
"It was very important how they reacted after Sunday. We needed to return to winning ways at home," said Simeone, who has overtaken Luis Aragones for the most wins in charge of Atletico with 309 in all competitions.
"What I liked the most was that it went from a bad moment with them the better team and well-positioned, to us being on top.
"The second half was very good, and we are now level with the others in terms of the number of games played."
Llorente's headed equalizer was his ninth LaLiga goal of the campaign, adding to his eight assists in what has been an impressive season for the Spain international.
Manchester United's Bruno Fernandes (26) is the only midfielder to have been directly involved in more goals in Europe's top five leagues this term than Llorente, who has emerged as one of Atletico's star men over the past year.
"Marcos, for a year, had no minutes. He was on the bench but continued training, working hard and had that will that leads you to be at this moment," Simeone said.
"He is very important for us and surely for the national team as well."
Suarez won the penalty that he converted – the striker being tripped in the box by Unai Nunez – and has now earned Atletico 15 points from his 18 league goals this term.
That is four points more than any other individual has won their side in the Spanish top flight in 2020-21, but Simeone reiterated Atleti's title charge is a collective effort.
"I look to the group as a whole because individuals alone do not change a game," he said.
"The team understood that we were not having a good time – they looked for order and then the group and the team generated a second half that we liked a lot."
Athletic were unhappy with the awarding of the decisive penalty and also argued that Llorente's goal should not have stood, coming as it did 17 seconds after the allotted two added minutes.
Marcelino, whose side are without a point away to Atletico since May 2015, felt the scoreline was harsh on his side as the hosts scored two goals from five shots on target.
"I am very satisfied with the performance of my side and I'm sad with the result because Atletico essentially took advantage of one hundred percent of their chances," he said.