The Welshman was sent to the stands during Stoke's 5-1 loss to Newcastle on Boxing Day after reacting angrily to the sending-off of Glenn Whelan.
Hughes, who is likely to face a fine, has until Thursday to answer the charge but confirmed he will accept it.
He said: "I got pulled up on the fact I kicked a ball onto the pitch. That's a fact, so there's no way around it. I can't really defend that, that's what I did. If that's what the issue is, I'm going to have to hold my hands up."
Whelan's sending-off was quickly followed by a red card for Marc Wilson, and Hughes was highly critical of the performance of referee Martin Atkinson.
Potters chairman Peter Coates said the club would be making an official complaint about Atkinson's display, and he and Hughes were also unhappy with referee Kevin Friend's decision-making during Sunday's 3-0 loss at Tottenham.
Hughes said: "Everybody has their own opinions but you just want performance levels to be at a good level.
"We're all judged on our performances - managers, coaches, players, and referees are judged as well. We just want good performances from everybody involved in the game.
"Over the last couple of days I've looked at certain incidents in some games in comparison to some of the decisions that went against us, and there were anomalies.
"At the moment a number of key moments in games have gone against us so we'd like that to change in the New Year.
"We're going to make representations to certain bodies because I think it's important that we don't just take it lying down. We feel as a club a little bit aggrieved by what we've gone through."
Hughes, meanwhile, was downbeat about the chances of significant additions to his squad arriving in the January transfer window.
A striker is the Stoke boss' priority, but he revealed no deals are close to being done after they were denied a work permit for USA international Juan Agudelo last month.
Hughes said: "There's nothing definite I can say that's in the pipeline for us at the moment. It may be a long window for us. We'd like to think we can do something."