In the 70th minute of the game between Hull and Manchester United at the KC Stadium substitute Hernandez was involved in an altercation with Jones.
The referee missed it and took no action at the time.
However the FA have confirmed today that Hernandez has been charged retrospectively.
He has until 6pm on Wesdnesday to respond.
Hull were relegated from the Premier League after the 0-0 draw on the final day of the season.
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