Trailing 1-0 from the first leg of their Copa del Rey quarter-final tie, Atletico were 3-2 behind at half-time at the Vicente Calderon.
The home side felt aggrieved that they had not been awarded a penalty with the score at 2-2 shortly before the break, and their mood was not improved when Barca broke upfield and took the lead for the first time in the match through Neymar.
Atletico had captain Gabi sent off at half-time as the two sets of players became involved in a brief melee when they left the field, and Simeone is alleged to have made a gesture in the direction of match official Jesus Gil Manzano.
"I didn't," Simeone said in a press conference. "That is a big lie."
Atletico must now turn their attention back to La Liga, with the champions visiting Eibar on Saturday.
"We're thinking of the Eibar match," he said. "We only care about playing a good match at a difficult field, against a team who've played well in the Primera Division.
"There's nothing else on my mind. Beyond their defensive rigour and tactics, which they have worked well, they are a team that have quality.
"On the wings, they have experience on the offensive side, they're a team that play well with the ball and know how to play in small spaces.
"They have people who work well and know the field. I don't think the match is only about intensity."
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