Benitez claimed he was more concerned at the penalty that got away rather than the challenge by Sergio Aguero on David Luiz that should have got the Manchester City man a red card.
Aguero headed City's winning goal to book an FA Cup final meeting with Wigan next month. But the striker also left his mark in another way, jumping on Luiz in a manner that would surely have led to his dismissal had referee Chris Foy seen it properly.
But Benitez was more frustrated at Foy's failure to spot City skipper Vincent Kompany grabbing Fernando Torres in the box, which would have provided the opportunity for Chelsea to level after they had fallen two goals behind.
"I don't like to point at players in this kind of situation," said Benitez of Aguero's second-half tackle.
"For me, the main one is the penalty not given. The consequence could have been a red card and a penalty. It could change the game.
"Yes (they got it wrong). It is something they have to clarify. I have seen the pictures. Kompany has the shirt."
Benitez said his challenge now was to keep Chelsea minds focused on the battle to clinch a place in next season's Champions League, which resumes with a trip to Fulham on Wednesday.
John Terry is likely to return for that one, having spent Sunday's game on the bench, prompting Benitez to defend comments made in an interview which suggested the inspirational Chelsea skipper was incapable of featuring in two games a week.
"I am surprised with the headline," he said.
"I tried to say that for some players, to play two games a week is not easy.
"It depends on the condition of each player. At this moment, Cahill, Ivanovic and Luiz are doing well, so we have to manage the squad."