The experienced frontman felt he had earned all three points for the hosts with a towering header, only for his effort to be ruled out for a debatable push on Brede Hangeland.
He hit out at Clattenberg after the goalless stalemate, claiming: "When I saw who was the referee I didn't expect to get anything off him. Over the years I have never got much from him.
"There was a penalty at Old Trafford last season and he did nothing - but I got a booking.
"Numerous bookings over the years - I don't know, I have always felt there is something personal there.
"Every time he referees us, I don't expect to get anything."
Davies now has until 12 March to respond to the charge, with the striker facing a fine and a warning about his future behaviour over the comments.
Bolton v Wolves 1st Goalscorer: Davies, K. 11/2