Simeone was sent to the stands in the early stages of an eventful game at Emirates Stadium on Thursday, having complained to officials following the red card shown to right-back Sime Vrsaljko in the 10th minute.
UEFA has charged the former Argentina international with insulting a match official and improper conduct, with a disciplinary panel to judge the case on May 4, the day after the second leg in Madrid.
"I don't feel good about that," he said.
"I understand that this can happen because things on the field go really fast.
"I know I have to improve myself in that aspect. I can't say anything - there's no excuse.
"When you are kicked out you can't say anything or justify anything, there's no excuses."
UEFA also charged Atletico for their fans throwing objects during the game, while Arsenal could be punished for their supporters setting off fireworks.