Mauricio Pochettino believes his men reacted late when Harry Kane lost possession of the ball, before United milked that moment to score the only goal of the match.
Herrera latched onto the mistake by Kane and sent a pass towards Mkhitaryan, who made no mistake in scoring his first goal of the EPL.
The goal was the difference between the two sides and gave United their first home win in a while. However, Pochettino defended his men.
He said: “It was an even game, very competitive. I’m not disappointed with our performance. We competed in a difficult game.
“The chances we create were similar to what Manchester United created but they were clinical.
“We had a lack of reaction when we lost the ball and that was how we allowed them to score. We need to understand that our offensive players need to take a risk.
“We tried to play with our philosophy and we tried to create chances.”