The 21-year-old came off the bench at half-time to help seal a victory that put Atletico five points clear at the top of La Liga with a game in hand.
Felix scored in the 69th minute and responded by putting his finger to his lips, unsmiling, and shouting in Portuguese in the direction of the Atletico Madrid bench before being surrounded by teammates.
"You'll have to ask him," coach Simeone said, laughing, when asked about the reaction. "He scored a great goal. He came on and did well in the second half... I love it when players rebel, when they look to be strong. We need him to be, he's an important player for us."
"I'll ask him in the next training session, and then I'll see if I tell you," Simeone added, when pressed on the celebration in his postmatch news conference. "I love it when players show pride. How long had it been since Joao scored? If players are rebellious, give them to me!"
Joao Felix cost €126 million when Atletico signed him from Benfica in July 2019 after just one year of senior football.
He scored six league goals in an inconsistent debut season and has seven so far this campaign, two of them coming in 2021.
The Portugal international has also struggled with a series of injuries and recovered from the coronavirus last month.
"He's a really important player," defender Stefan Savic said. "He's different, with an incredible talent. I don't think [the celebration shows that] he was annoyed with anyone. He knows the important role he has here."
Another teammate, Luis Suarez, posted a photo of himself and Felix smiling together after the match on social media.