The pair have been charged for comments after defeat to Everton.
The FA said: "It's alleged that the club, manager and player's comments constitute improper conduct in that they imply bias and/or question the integrity of the match officials and/or bring the game into disrepute."
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They have until Thursday to respond to the charge.
After the defeat, Williams said: "Every single week this happens now. We are getting decisions against us, I don't know why. Is it because we are a lower, bottom half of the table team? Because I guarantee all the top six teams are getting every single one of them.
"I know every single person watching that game today knew all three of them were clear, blatant penalties. It is ridiculous. It is week after week now we are getting these decisions against us."