Jean Tigana watched Fulham lose out at the Riverside after Steve Marlet put the Whites back on level terms after Alen Boksic gave the home side the lead.
In a game where Fulham had the upper hand in terms of possession, the match arguably took a different course after decisions from referee Dermot Gallagher.
With Boksic's goal carrying a suspicion of offside, Tigana took an understanding stance to referee Gallagher's judgement. However, other aspects of the game were not as clear to the Whites manager.
"I didn't blame the referee for Middlesbrough's opening goal. We all make mistakes. But there was a real problem when he did not allow us to play on after a Queudrue foul in the second half. From the free-kick we didn't even get a corner after the ball came off the defensive wall.
"I don't understand why at the end, we had a chance to score and he stopped the game and didn't give the defender a yellow card," he said.
"I never discuss the referee when it's a penalty or an offside, but this action is difficult to explain to my players because we could have scored. The referee, the same as a player, can make a mistake. That's life, that's football.
"But I have to disagree with that last action because I don't understand why he stopped the game when we had an advantage. We had the chance to score, and normally if you stop the game, you give a yellow card. That for me is a big mistake."
Mindful of the frustration that his players were feeling straight after the match, Tigana prevented them from coming into contact with Gallagher.
"I made sure my players did not go to the referee after the game. We only have a small squad and I did not want the referee taking any further action."