Luis Suarez headed in a 97th-minute equalizer at Anfield after Eden Hazard's penalty looked to be the winner and the former Reds manager was shocked at the amount of injury time.
The former Reds boss thought that his new side would snatch all three points on his return to Anfield after Eden Hazard's second-half penalty but the Uruguayan leveled after the 96th minute to steal the headlines.
Benitez, whose hopes of a top-four finish were damaged by the late strike, says that he cannot understand from where the six minutes came.
"I was disappointed with the late goal conceded," he told the club's official website, "especially because I can't understand why there were six minutes and 45 seconds [stoppage time] - a very strange decision.
"Some games you have six substitutions and they say three or four minutes. In this case, six minutes, a throw-in for us and the game was over - and still 45 seconds more. It is difficult to explain."
Former Chelsea player Daniel Sturridge set up Suarez's equalizer with a cross from the right, having hit the post in the game earlier on, and Benitez admitted that his side's defending could have been better.
"We have to analyze why we didn't stop the cross and why Liverpool scored but still, in the normal circumstances, we would have finished the game having won against a good team," he lamented. "They were pushing but we were defending well and had our chances in counterattack in terms of dangerous situations.
"Sometimes when they try to explain added time they put substitutions as 30 seconds, sometimes they say 40 seconds, sometimes one minute - but every single game you have three or four minutes added, five minutes if it is a lengthy incident - but six minutes 45 seconds?"