The Spanish midfielder appeared to be brought down by Nicolas Otamendi in the box but referee Michael Oliver instead opted to show a yellow card to Herrera for diving.
The spot-kick would have presented the Red Devils with the opportunity to snatch an equaliser in the closing stages of the game against Pep Guardiola’s men.
As it finished, the Red Devils slumped to a disappointing defeat by their bitter local rivals as they fell 11 points behind them in the table.
Herrera admits that he was shocked to be shown a yellow card for diving and remains convinced that it was a penalty.
Herrera is quoted as saying for Sky Sports: “I think the penalty [decision] is amazing. He didn’t expect to arrive for the ball. I touched the ball first and he stamped on my foot. I think everyone saw it.
“Everyone can make mistakes too, also the referee. I didn’t deserve the yellow card. In the first half, there were similar situations with Gabriel Jesus and Leroy Sane, and they didn’t get yellow cards.
“That is my fourth yellow card and that is a big problem for me.”
The midfielder will be hoping to start for Manchester United when they attempt to return to winning ways in the Premier League with a home clash against Bournemouth on Wednesday night.
The Red Devils have not won the Premier League title since their famous final triumph under Sir Alex Ferguson back in 2013.
Manchester United finished sixth last season but won both the League Cup and Europa League under Jose Mourinho.
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