Rumours of a heated training-ground exchange between Chelsea's interim manager and his senior players appeared in the national press less than 24 hours after their 2-0 defeat at Manchester City.
Terry was on the bench at the Etihad Stadium, and the captain's lack of playing time since returning from a knee injury in January has led to claims of a strained relationship with Benitez.
Both men rubbished those reports earlier this month, and Benitez continues to insist there is a "really good atmosphere" in the dressing room.
He said: "This was a normal meeting between players and technical staff, which happens after every game. It was normal talk, nothing else. You show your disappointment, that is normal.
"I can understand the frustration of Terry, an important player for us who's trying to help and push because he wants to win, but he has been injured for 16 weeks and has had problems with his knee.
"He's missed some training sessions. So we are managing him. He wants to win, but we have to manage our players.
"It was very brief exchange of ideas, and that is it, nothing else. It is just a team talk after a defeat. We had a meeting on the training pitch with my players and technical staff, which is part of our business."
Asked about his relationship with the Chelsea players, Benitez said: "It is fantastic. I have no problem."
Benitez maintains everyone is united at the club to make sure they end the campaign on a positive note, having slipped down to third in the table following Tottenham's late win at West Ham.
"They are a good group of players, working hard and keen to learn. They were disappointed like me with the defeat, but that's it," he said.
"(We want to finish in the) top three, it is really important for us but, being a top side, we have to try and win every game.
"Middlesbrough were doing really well, but they have also had some games with problems.
"They have a good manager and a good team. They will give everything in the FA Cup, so it will be difficult."
With Chelsea continuing their progress in Europe, a replay in the FA Cup would be the last thing they need, should the Blues fail to set up a quarter-final tie with Manchester United at the first time of asking.
Benitez, though, maintains the team will only be looking to the next match on what is fast becoming a packed fixture list.
"We will try to win, for sure, that would be better, no? In my head, the only thing is just to win," he said.
"The team that has played more games in Europe is Chelsea, but we have to carry on and manage the squad as well as we can.
"It is not ideal, but it is something we have to do. We have done it in the past with top sides and we will do the same."
Centre-back Gary Cahill has a virus, while full-back Cesar Azpilicueta has "discomfort in his leg", so Benitez will have to make some adjustments in defence.
Terry played for the Blues against Sparta Prague in their Europa League last-32 second-leg clash last week, but Benitez warned the former England skipper must continue to be carefully managed.
"He had the plan before and we have to decide (what is best)," Benitez said. "He was training (today) and could finish the training session today, so he could play (at Middlesbrough)."