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 (the penalty)?
“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 per cent 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,” Agnew added. “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: “(On Monday) we will see but I think he has got a leg injury. But I don’t know - (on Monday) 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.