Benitez was unhappy with Liverpool's performance against Liege, but Agger insists he did not have a confrontation with the Spaniard after the game in Belgium.
"Of course there are things that Benitez was not satisfied with after Liege," Agger told Danish TV station TV3.
"We didn't play a good match, but it is a big lie to say we had an argument. I certainly hope it is only football reasons why I am not playing.
"I have no problem in this club. He has just said that the team is playing very well, and that is why I am not playing."