Steve Agnew blasted Leroy Sane after his tumble to win a penalty.
The Boro boss reckoned the City midfielder “went down too easily” when he clashed with Marten De Roon.
The penalty gave City a lifeline and the game ended in a draw, virtually condemning Boro to relegation.
Agnew, whose side put on their best show of the season, said: “Penalty? I didn’t think it was. The player went down very very easily.
“Was the referee (Kevin Friend) in the correct position to give it? The video I have seen looked like he didn’t have a clear view and if you give them you should have.
“Once it has been given I was pleased with the reaction to get a second goal.
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“The performance showed the determination and fighting spirit of the players we have been working with for the last few weeks. That was evident against one of the top teams in the country.
Boro could be nine points behind fourth bottom if Hull beat Sunderland next Saturday, before they face Chelsea on Monday with three games left.
Agnew added: “We are six behind with three games left and a good goal difference. My players will take confidence going there having played well against City.”