Boro were 1-0 up at the Riverside Stadium through Alvaro Negredo’s early strike when referee Kevin Friend pointed to the spot after Marten de Roon collided with City substitute Leroy Sane in the box. Sergio Aguero made no mistake from the spot, converting in the 69th minute.
Calum Chambers put Boro back in front only for the returning Gabriel Jesus to salvage a late point for the visitors in a 2-2 draw.
Agnew said: “I thought (Sane) went down very, very easily — and looking at the referee’s position, was he in the correct position to give it?
“From the video I’ve seen it looked like he didn’t have a clear view and I think when you give them, you’ve got to be 100% certain.”
Agnew admitted his frustration after what was arguably his side’s best performance of the season left them six points off safety with just three games to go — with champions-elect Chelsea next up at Stamford Bridge.
“I was very disappointed that we didn’t see the game out,” said Agnew. “I thought the lads were terrific and they deserved the three points.
“I think the performance today just showed the determination and fighting spirit of the squad and the group of players I’ve been working with in the last few weeks, and that was evident against one of the top teams in the country.
“I think the message has been the same in recent weeks — it’s one of being organised and disciplined. We’ll continue to do that and I’m very, very confident we will get the results we need.”
City boss Pep Guardiola shrugged off questions about the penalty controversy and instead focused on the fitness of Aguero, who limped off in the final minute of the game with what appeared to be a groin strain.
Guardiola revealed Aguero will undergo tests today to determine the nature and extent of the injury, amid fears he could miss out on part of his side’s run-in as they look to secure a top-four finish.
Guardiola said: “We will see but I think he has got a leg injury. But I don’t know — we will make the assessment.”
City next face three consecutive home games against Crystal Palace, Leicester, and West Brom, and Guardiola believes the results of those games will determine his side’s European fate for next term.
Guardiola said: “Now we have three games at home and those three games will decide whether we deserve next season to be in the Champions League or not.
“Today it was in our hands to fight for the third position and we have dropped that position. Now we have got to win games and make some good results at home.”
Despite frustration at not coming away with three points, Guardiola said he was broadly satisfied with his side’s performance, after starting with both Aguero and the recalled Jesus for the first time.
Insisting his side deserved to win, Guardiola added: “We made absolutely everything, they crossed the line twice and nothing else and we created an awful lot of chances in the game.
“We have three games at home but all the games are tough. We cannot forget that when we come here they are fighting to survive in the Premier League and when you face this kind of team it is the most difficult.”
Guzan, Da Silva, Chambers, Gibson, Friend, de Roon, Clayton, Forshaw, Stuani (Traore 73), Negredo (Gestede 82), Downing.
Caballero, Otamendi, Kompany, Kolarov, Jesus Navas, Fernandinho, Garcia (Sane 50), Clichy (Sterling 50), De Bruyne, Aguero (Nolito 90), Gabriel Jesus.