Benitez rued Chelsea's defensive failure at the end of the match after his side were in control of proceedings throughout at the Madejski Stadium and also explained his reasons in bringing off Mata with just over 10 minutes remaining.
"It's difficult to explain because we had a lot of chances," he told Sky Sports. "We could have killed the game.
"We conceded two late goals. Especially the last one, a free-kick from the middle of the park. It's difficult to explain.
"They have two players at the back post and we didn't have anyone around. It was a big mistake and we paid for that.
"It was 85 minutes and we knew that it could be this kind of situation. We had to keep the ball in the last minute and score the third goal.
"We changed Mata because he was limping. He had a problem with his ankle. (Demba) Ba could hold the ball in the last few minutes.
"Everything was under control, just the last ball and we didn't have a second player on the back post.
"We controlled everything. We were doing a great job as a team. We couldn't win because of this mistake and we couldn't take our chances."