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And Mexico were eliminated from the World Cup after Klaas-Jan Huntelaar converted the spot kick following a challenge on Robben from Rafael Marquez.
But Hernandez refused to blame referee Pedro Proenca for his side's exit from the tournament, despite being less than convinced by the decision.
"A loss is a loss, we were so close to getting through and we couldn’t do it, then a very doubtful penalty took us out," he told reporters.
"We can’t manage referees, they are humans. Unfortunately sometimes some mistakes hurt a lot of people; a country.
"It’s not about assigning blame. As I said, they are human, today we got a bad decision, what can we do? We can’t do anything."
Hernandez was left to rue the defending which allowed the Dutch a way back into the game through Sneijder's late strike, but believe fans can make up their own minds on whether or not Proenca made the correct call.
He added: "Football is this way. You can’t predict anything, unfortunately we had a distraction in the marking and then a doubtful penalty.
"The images are there, people will see if it was a penalty or not."