Chicharito was caught by the despairing challenge as he fired into the side-netting when looking to profit after Wayne Rooney's shot bounced back off a post with 13 minutes remaining.
It upset and puzzled Sir Alex, who saw the full-back booked but, as no penalty was awarded, there needs to be some clarity from referee Phil Dowd on the situation and whether the yellow card was for dissent.
"To me, it was a shocking tackle," protested the boss. "An absolutely shocking tackle.
"The referee's booked him and, if he's booked him, I don't know why it wasn't a penalty.
"I must ask him [Dowd]. We don't know how Hernandez will be. We're going to have to wait until the morning but, at the moment, his leg is very numb. He's hardly got any feeling in it so he could be out for a couple of weeks."
Sir Alex felt Cole's tackle was "reckless" and "over-committed" and could also be missing Chris Smalling for the upcoming matches against Leeds and Stoke.
"Smalling's got a groin injury so we'll see what it's like during the week," he added.