In Salvador on Monday, a Thomas Muller hat-trick guided Die Mannschaft to a comfortable win over Bento’s side, who will be without Pepe for their remaining group games after the Real Madrid defender was sent off by Serbian referee Milorad Mazic following a clash with the Germany forward.
Muller also converted a 12th-minute penalty after Joao Pereira was adjudged to have brought down Mario Gotze in the area, and Bento believes both decisions cost his side the game.
"These were the two things that seemed to show bias and they were both decisive," he said.
"The penalty was forced and I don't know if (Pepe) was sent off because of his reputation.
"I'm not saying it was the referee's fault only. We did make mistakes, not only in our defence but also in the sharpness of our attack."
Bento admitted that his side will have to extensively examine their defeat if they want to qualify from Group G – which also features Ghana and the USA.
"We're going to have to analyse this game in depth," he said.
"Of course, we're very disappointed. We tried a few things in the second half, but the game was already lost by then.
“There was nothing more we could have done. Apart from the first five minutes, we were just not in the game."