Despite dominating, Yossi Benayoun's 41st-minute goal from a narrow angle was all the visitors had to show for their efforts and it was not enough.
In the closing stages Wigan sensed they had a chance and, when Brazil midfielder Lucas needlessly brought down substitute Jason Koumas, debutant Mido, signed on loan from Middlesbrough last week, converted from the penalty spot.
It condemned Liverpool to their seventh draw in 10 Premier League matches and their fourth on the bounce in all competitions.
There was a suggestion Wigan midfielder Michael Brown's over-physical treatment of opposite number Steven Gerrard had upset him but Benitez refused to comment.
"No I am disappointed with a number of things but no, the Wigan approach I will not talk about them," he said.
"It has happened in the last three games. They have something in common I don't like. I know why but I cannot say anything.
"The players were okay. They were working very hard in the first half but the second half changed because it was crazy.
"I was talking with my players about what to do on the pitch but there are things that you cannot control."