The Real Madrid defender appeared to inadvertently handle the ball inside the penalty area towards the end of Los Blancos' 3-1 win over Eibar on Sunday, but escaped punishment from referee Jose Luis Munuera Montero as well as VAR.
Madrid's fifth straight win in all competitions left them level on points with Atletico but Koeman hinted Los Blancos were fortunate.
"I saw the incident and, for me, it's a penalty," Koeman said ahead of Barca's trip to Valladolid on Tuesday.
""The day of the Madrid match, I said something that doesn't need to be repeated.
"I think there are things that cannot be understood. I'm sure that if you ask 10 people if yesterday's game is a penalty, nine would say it was.
"However, the referee and his team decided not to call it."