Nathan Jones felt Luton were hard done by at the Riverside Stadium as Middlesbrough secured a narrow win after a controversial finish.
The Hatters boss and his players were left angered when referee Andy Davies initially allowed James Collins' equaliser from the penalty spot with 23 minutes remaining, only for it to then be ruled out.
Davies' assistant Akil Howson, who did not immediately signal an infringement, agreed with Boro's complaints that Collins had taken a double touch and it was chalked off.
Middlesbrough held on to a lead secured by Chuba Akpom's 52nd-minute opener with some game management to run the clock down, which Jones was annoyed that the officials did not control better.
"I haven't seen it (the penalty) yet, it obviously touched his foot so it was the right decision," said Jones.
"The assistant didn't give it until they remonstrated with them (officials), then he changed his mind. At no point did he (Howson) flag. They persuaded him to change his mind. If it is the right decision, fine, but that was what I was angry with. It is difficult.
"There were two things I was disappointed with, one was our tempo and the way we started the second half, the other was the way the game panned out. I think the ref could have handled that better.
"Middlesbrough did the professional thing to slow the game out. The ref is in charge of the tempo and it was borderline a joke.
"I know why they did it. Since the penalty, the sending off, I will be surprised if the ball was in play for more than seven or eight minutes for near enough the 35 that was left and that's not right.
"When you are down to 10 men, fighting for your life, every point is important, then there was no flow in the game. I felt the ref could have managed it better.
"As soon as there was a corner players were falling down, there were a lot of breaks like that. That's what I felt the ref could have handled better, the game petered out. It wasn't a spectacle in the end."
Middlesbrough were on the wrong end of a decision like Collins' last month when Marcus Tavernier had a penalty ruled out against Norwich for a double touch when he slipped.
Boro boss Neil Warnock was happy to be on the right end of a decision this time and was pleased with how his side held on to climb up to seventh.
Warnock, who saw midfielder Sam Morsy sent off for handball in the penalty incident, said: "After that finish, wow. I am so proud of the lads, the penalty, how we reacted to playing with 10 for such a long time, they defended for such a long time.
"I am disappointed, if I'm honest, with the red card. I'm not sure if the referee is in a position to give it. Sam had been pulled by a white shirt, he fell, then it hits his arm.
"Luton have appealed for every decision, that swung the decision really. Thankfully, when they took the penalty, the ref didn't disallow it but the linesman was excellent looking at it.
"He definitely touches it twice, easier to tell than the one we had against Norwich. People will say lucky but I would say it was just.
"I will have a word with (chief executive) Neil (Bausor), definitely worth an appeal. It looks more obvious from behind. I will have a word with him. One-game ban, do we let him have a rest?"
