Hernandez was forced off due to injury in the second half of United's fifth straight win of the season after being on the wrong end of what Sir Alex Ferguson felt was a "shocking tackle" from the England full-back.
However, Villas-Boas felt the incident might not have happened if the officials had got two earlier offside decisions correct, which would have wiped out goals for Chris Smalling and man-of-the-match Nani.
"Maybe he wouldn't get sent off if the linesman does his work," said Villas-Boas. "He [Cole] would have been less emotionally drained.
"I work the other way round. You are trying to say the referee did something wrong. I cannot forget the previous two.
"If it was 0-0 maybe Ashley is a little bit more mentally in control of the situation and doesn't do the red card foul that you mention."