The alleged offence, contact with the eye area of an opponent (Law 9.12) took place in the 37th minute of the match.
A disciplinary hearing will be convened before a Six Nations Disciplinary Committee on Wednesday.
Before the match started Wilson was also involved in an off-field incident.
England centre Owen Farrell and Wilson appeared to become embroiled in some pushing and shoving as the two teams left the field following their pre-match warm-ups.
A statement provided to Omnisport on Sunday read: “Six Nations Rugby will be writing to the unions to request clarification on what happened in the tunnel.”
England coach Eddie Jones denied any knowledge of a scuffle, while Scotland captain John Barclay was quoted by the Guardian as saying: “I heard about it but I am always the first off the pitch after the warm-up and I was in the toilets.
“It is one of those things that gets built up into something more than it was.
“It is a big game and a big rivalry. It was niggly and physical with a lot on the line.”
Scotland went on to beat England 25-13 to win the Calcutta Cup for the first time in 10 years and end their rivals’ hopes of claiming a Grand Slam.
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