The Mexican went to ground under Danny Simpson's late challenge and was booked by referee Lee Probert, who had earlier turned down a similar appeal from Magpies' frontman Peter Lovenkrands.
Ferguson was adamant the Barclays Premier League leaders should have been awarded a spot-kick and the chance to extend their advantage over second-placed Arsenal to nine points, and suggested officials should recognise the character of the players with whom they are dealing.
He told MUTV: "To book the player, he gets himself out of jail in people's eyes by doing that, and it's disappointing because he had an outstanding game, the referee.
"I thought he was one of the better ones I have seen this season to be honest with you, I thought he had a really good game.
"Know the players you are refereeing. You would think the preparations for referees should be the same as a manager - prepare yourself, know each player in each team. He [Hernandez] is not that kind of player."
Source: PA