Swiss defender Philipp Degen and captain Jamie Carragher were sent off for second-half fouls as Liverpool's Premier League hopes disintegrated, falling to their fifth league loss of the season, but Benitez believed referee Lee Mason got both decisions wrong.
Benitez said: "They were two incidents in a few minutes when we were losing and they were difficult to take. The first one was a yellow card. The second one you can clearly see that Carragher was kicking the ball."
Bobby Zamora put Fulham ahead and Fernando Torres equalised in a first-half in which Liverpool dominated possession.
But when Erik Nevland put Fulham ahead for the second time and Torres had been substituted there was only one winner, Clint Dempsey scoring a late clincher for the home side.
Benitez, however, was left wondering how Liverpool could have lost after enjoying so much possession.
He said: "It's hard to take the defeat, especially when we were in control of the game. The first half was one-sided. We made one mistake and we conceded a goal.
"The second half they were more offensive and we made a massive mistake when we conceded the second goal. We worked hard with nine players but it was very difficult."
Benitez could now be without Torres and Steven Gerrard for the crucial Champions League clash against Lyon on Wednesday.
The Liverpool boss said he would "have to see how Gerrard progresses" with his troublesome groin injury, while Torres is still not fully fit.