"It was a normal meeting between players and technical staff that we have after every game...nothing else," the Spaniard told a news conference ahead of holders Chelsea's FA Cup fifth-round tie at second tier Middlesbrough on Wednesday.
"To show your disappointment after a defeat is normal. I can understand (John) Terry's frustration because he is an important player for us.
"He is trying to help because he is trying to win and I can understand his frustration because he's been injured for 16 weeks with a knee problem," added the Spaniard, the ninth Chelsea manager since Roman Abramovich bought the club in 2003.
Former England captain Terry, 32, has been a regular starter at centre half throughout his one-club career at Stamford Bridge but he has been left on the sidelines by Benitez in several recent games.
"He has missed some training sessions and has had special treatment on his knee," said the Spaniard. "We are managing him.
"We know he wants to win and it is normal to share opinions. But we have to manage the fitness of our players and we have to manage our squad. We had an exchange of ideas and that's it."
Benitez denied there was a problem in his relationship with Terry and also scotched the idea that he had talked to his players about previous Chelsea managers.
"I have a fantastic relationship with the players," said the former Liverpool, Inter Milan and Valencia manager. "We are training really well.
"I've said it before and I'll say it again, the atmosphere is really good. I have a good group of players, they're working hard and are keen to learn.
"After a defeat we have to be disappointed and they were disappointed just like me - but that is it."
Terry was rested for Sunday's Premier League game at City but is almost certain to return at Middlesbrough with England centre half Gary Cahill sidelined due to a virus and Spain full back Cesar Azpilicueta missing with a leg problem.