The 53-year-old thinks one of the Manchester City manager's back-room staff should have informed him that a 4-2 win against Bayern Munich would have seen his side top the group
City beat Bayern Munich 3-2 at the Allianz Arena on Tuesday but a 4-2 win would have seen them finish top of the pile, with Pellegrini's men eventually finishing runners-up.
And Benitez, whose Napoli side were knocked out due to an inferior three-way head-to-head record with Borussia Dortmund and Arsenal, is surprised Pellegrini was not informed of the standings by one of his coaches.
"As a manager, you need to be thinking always about tactics and ways of playing and sometimes you need your staff to help you with details like the calculations," he wrote in The Independent.
"It is better to know everything as a manager, maybe, but Manuel Pellegrini needed one of his staff to tell him the mathematics in Munich.
"It mattered – because there’s a big difference between winning the group and coming second in the group. Just look at the list of teams on those two lists and you will see why."
Benitez also offered some encouragement to England boss Roy Hodgson, suggesting that the Three Lions have every chance of beating Italy in Manaus at the World Cup as long as they prepare correctly.
"I didn’t think we would be talking about England playing Italy again quite so soon. I must say what I think, of course. Italy are a better team than they were back at Euro 2012," he continued.
"I have seen a little bit of talk about Andrea Pirlo being injured but they say here in Italy that he will only be out for two months, so I don’t think there can be an expectation that he will not be there in the Amazon.
"The team has players who can change games. We talked about Mario Balotelli here a few weeks ago and how he has improved. Italy are used to playing to the maximum level and controlling games. They are good tactically and adapt well.
"But none of that means that England cannot do well. When the pressure is off and no one has big expectations, it can help to set you free as a team. There is always a chance in the game of football if you investigate a way of playing and make sure the preparations are right."