Mexico striker Hernandez limped off the pitch towards the end of the match after a late tackle by defender Ashley Cole who smashed into his shin, while defender Smalling was substituted earlier with a groin injury.
"To me, it was a shocking tackle," Ferguson said of Cole's challenge which came as Hernandez was attempting to shoot at the back post off a rebound.
"The referee's booked him and, if he's booked him, I don't know why it wasn't a penalty. 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."
The referee did not give a penalty because the ball had just gone out of play.
United, who travel to Leeds United in the League Cup on Tuesday before heading to Stoke City in the league on Saturday, could also be without England's Smalling for those games.
"Smalling's got a groin injury so we'll see what it's like during the week," Ferguson said in comments posted on the club's website.
United went two points clear of neighbours Manchester City at the top of the Premier League with Sunday's victory over third-placed Chelsea where Smalling had opened the scoring with an eighth-minute header.
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