The Mexican international appeared to be in front of the last defender as he poked home in the 75th minute at Stamford Bridge after United had let a two-goal lead slip.
When asked if he was offside, Hernandez told Sky Sports News: "Probably. I think it's a habit that I have to look to the linesman.
"For us, we won the three points and it is very difficult to come here to Stamford Bridge and take the three points, and we're very lucky and happy with that."
Sunday's win has seen United return to second place in the Premier League table.