Ferguson berated assistant referee Simon Beck for not giving his side a penalty following a foul on striker Wayne Rooney, an incident that could have given the visitors a good chance of taking a 2-0 lead.
"It was a clear penalty kick on Wayne Rooney but in no way was the linesman going to give that," Ferguson told Sky Sports.
Ferguson has until 18:00 GMT on Thursday to respond to the FA's enquiry.
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