Sanchez Flores was furious with Espanyol midfielder Javi Lopez for what he felt was time-wasting and a lack of respect and clashed with opposing captain Luis Garcia before being dismissed from the bench.
He had to be restrained by Espanyol goalkeeper Carlos Kameni and other players and officials when he tried to confront Garcia again after the final whistle.
"It seems unsporting to me, they were mocking us with this behaviour," he told a news conference after the match, which left Atletico in sixth on 20 points from 13 matches and Barcelona-based Espanyol in fourth on 25.
"It's important to know how to lose but it's also important to know how to win," he added. "I will accept whatever punishment that comes."
Garcia said he had been surprised by Sanchez Flores's attitude as the Atletico coach had previously seemed an "educated person who respected the other team".
"I think it was a mistake on his part, nothing more," he told reporters.
"I did not laugh at anyone, nor at a club as important as Atletico," he added.
"I did not manage to talk to Quique at the end of the game and only wanted to congratulate my team-mates. I imagine I will talk to him."
