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 in Moscow, 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.
"I'm really pleased with the team, with the effort, with a lot of players. They were giving everything on the pitch.
"We managed the squad and hopefully we'll have some fresh legs for Sunday too."
It appears unlikely Chelsea captain John Terry will start against City, having been in and out of the side of late.
Terry was at far from his best on a collectively shaky defensive display and it is rare to see a defence featuring the former England captain dominated in the air.
"I'm disappointed, because we didn't defend well second half, but still we go through," said Benitez, who praised 18-year-old midfielder Nathan Ake and Paulo Ferreira, who played at left-back due to the absences of Ashley Cole (hamstring) and Ryan Bertrand (illness).
"We have to improve on the second half, but not just the defenders, the team defending.
"We have to stop crosses, we have to deal much better with the crosses, things we couldn't do.
"Also you have to give credit to them. They have some players with quality and some of the deliveries were very good too."
Torres was the difference in the tie, but perhaps his fourth-minute goal - his 19th of the season, fourth in three Europa League games and a strike which meant the Russians needed three to force extra-time - released so much pressure that Chelsea eased off and allowed Rubin's second-half flourish.
The Spaniard showed the finishing instinct which has so often been lacking during his spell at Stamford Bridge since his £50million transfer from Liverpool when he was found by Lampard's exquisite pass and lofted the ball over the advancing goalkeeper.
Benitez has often rotated Torres and Demba Ba, who is ineligible in Europe, but may be considering leaving in the Spaniard at Wembley, particularly as Ba is recovering from an ankle knock.
"Fernando did really well," Benitez said.
"He's been doing well in the last games, he's working hard, he's creating chances for himself and his team-mates.
"We will think what we have to do for Sunday. Still we need to check how Demba is and afterwards we will decide."
The true bounce on the synthetic surface might have worried Torres as he wheeled away and looked over his shoulder before seeing the net bulge and Benitez repeatedly mentioned the pitch afterwards.
"It's the same for both and we have to adapt to these conditions, but still it's not ideal for us, because we normally play on natural grass," Benitez said.
Rubin had already eliminated 2012 Europa League winners Atletico Madrid and they were seeking to add the Champions League holders to their list of conquests, but were narrowly denied.
Rubin Kazan coach Kurban Berdyev said: "I have mixed feelings. We won but I'm really sorry we couldn't make it through.
"On the other side I'm satisfied with the game, especially the second half.
"Unfortunately we made mistakes which we usually don't make and Chelsea can punish and they punished us for our mistakes."