Benitez saw key men miss the trip to Villa Park through injury and was forced to make do without goalkeeper Jordan Pickford, defender Seamus Coleman and attackers Richarlison and Dominic Calvert-Lewin.
The Everton boss shuffled his pack, but saw his side slip to a 3-0 loss as Matty Cash, Lucas Digne (own goal) and Leon Bailey struck in a nine-minute goal blitz in the second half.
The defeat is Benitez’s first of his Everton reign and the Spaniard feels if his side had used several situations differently then the outcome could have been different.
“I think that we started the game quite well, we had a lot of situations on the counter in the first half and the final decision was not right”, Benitez told the BBC’s Match of the Day programme.
“We had a couple of chances in the second half then conceded and again soon after.
“We started with too many problems but the team was fighting well.
“Sometimes if you have players you can make situations and have fresh legs. In some positions we were short of legs.
“Salomon Rondon, Demarai Gray, Alex Iwobi, we had some situations where it could have been different.
“We made mistakes too soon, too early, too close and it was difficult to react. Hopefully we can manage that in the future”, he added.
Everton now have a quick turnaround with an EFL Cup tie on the agenda against QPR and Benitez will be hoping to make progress in the competition.