Frank Lampard and David Luiz had a heated exchange while leaving the Luzhniki Stadium pitch at half-time, when Chelsea led through Fernando Torres' fourth-minute strike.
The second half was fraught for the Blues as Ivan Marcano and Gokdeniz Karadeniz scored headers either side of Victor Moses' curled effort and Bebras Natcho netted a 75th-minute penalty to set-up an anxious conclusion, which ended in a 3-2 win for Rubin, but a 5-4 aggregate success for Chelsea.
"It's always good to have players arguing about things that can happen on the pitch," Benitez said.
"You can correct these things at half-time. We were talking about that, we were adjusting positions and I think it's fine, so it's not a problem."
Chelsea are now in a third semi-final of the season - four, if you include the Club World Cup - after advancing to the last four of the Capital One Cup and FA Cup, but must improve for Sunday's Wembley semi-final with Manchester City.
Benitez was not too downbeat about the loss, which followed Chelsea's 3-1 win at Stamford Bridge a week ago.
"You have to analyse the two games in context," added Benitez after Chelsea's 58th game of the season.
"We had a good result coming here, a different environment and different things we had to manage.
"I think we did well. It's a pity we lost the game, but we went through, that was the main thing."
- Sports & Recreation