The game's key talking point came in the 34th minute when Bertrand was penalised for pulling back Raul Rusescu, who converted the spot-kick.
With Bertrand as the last man and preventing a possible goalscoring opportunity, there were calls for him to be dismissed, but referee Sergey Karasev booked the left-back to Benitez's consternation.
"I think it was very soft. To give a penalty in this situation, and especially when you have so many referees in their positions, it is soft," the Spaniard told ESPN after the Europa League last-16 defeat.
"You cannot change the situation but it is very soft.
"If you give the penalty, why not the (red) card? Strange."
Benitez thought Chelsea were the better team on the night but rued their lack of a cutting edge in the final third, meaning they have it all to do at Stamford Bridge in the return leg to keep their hopes in this competition alive.
"I think it was a difficult game," he added.
"The pitch was not the best but we were disappointed because we conceded a goal because of a soft penalty and I thought their keeper made one or two good saves.
"It was difficult because in the counter attack they were dangerous but our keeper was not making any saves.
"I was a little bit disappointed because I felt we could have scored and now we have to do everything at Stamford Bridge.
"It will be difficult because they are quite organised, they work very hard and they can counter-attack.
"But we have confidence that we will do well at Stamford Bridge."
Petr Cech echoed Benitez's comments, believing the Blues deserved something from the game, but the goalkeeper is confident ahead of the second leg in London next week.
"This is not the result we want to get away from home in the first leg but to be fair we had better chances than them," said Cech.
"I hardly made a save all game. They had a penalty and they scored from there and they won. We're just disappointed we didn't score.
"We made it hard for the return leg but 1-0 is not the result you can't overcome."