Koeman's frustrations boiled over late on when he was sent to the stands by referee Pablo Gonzalez Fuertes after a confrontation with the fourth official. Fuerte's match report said he dismissed the Dutch coach for saying "What a character" to his assistant following repeated warnings about his behaviour.
"According to the report I disrespected the fourth official," Koeman said in his postgame news conference. "I don't understand because I didn't insult him at all. If anything, the way he spoke to me was disrespectful.
"I spoke to him about various incidents but always respectfully. I'd like to know what words I supposedly used because I didn't say anything ugly. It's incredible. But if the fourth official wants to be the centre of attention..."
Pending an appeal, Koeman will be unable to sit on the bench for Barca's next two games against Valencia and Atletico Madrid as the La Liga title race moves into the final stretch.
Even a draw against Granada would have kept Barca's fate in their own hands, given they host Atletico on May. 8, but they're now dependent on Madrid dropping points as Los Blancos have the superior head-to-head record between the two teams.
Koeman blamed the shock defeat to Granada on sloppiness in defence.
"We dominated the first half and should have scored one or two more so we could relax a bit more at the end of the game," Koeman added.
"Analysing the two goals we conceded, it was down to a lack of concentration in defence. That's what's cost us the points. We didn't defend well, cut out passes or close down spaces.
"It's a big disappointment. It's a setback because we don't depend on ourselves anymore. We have to pick ourselves up, look at what we've done wrong here and then prepare for a crucial game on Sunday [at Valencia]."
Messi's 26th goal of the La Liga campaign looked to have set Barca on track for the top but he missed the chance to double his side's lead and Antoine Griezmann, who brilliantly set up Messi's goal, also missed a good opening early in the second half.
"It's a bad day," defender Jordi Alba said. "We tried until the end, but we weren't clinical. It was a unique opportunity to go top and now we don't depend on ourselves anymore.
"[Granada] basically got forward twice and scored twice. I think we have to kill games off sooner. This is a big blow, but we must win our remaining five games now. There's nothing else for it."