England were 21-0 up when Ben Youngs thought he had secured the bonus point for the hosts.
The Leicester Tigers scrum-half raced onto Jack Nowell’s through ball after good work from Elliot Daly and the official initially gave the try.
However, upon review, the New Zealand referee was informed to reverse his decision because of an alleged knock-on.
While Williams was being told of the incident, England fans inside Twickenham were shown the ‘try’ on the big screens.
And they cheered every time Youngs placed his hand on the ball as the effort seemed legit.
The home supporters were shocked when it was ruled out and they booed the decision.
However, they did not have to wait long for the fourth try of the afternoon.
Wing Jonny May was once again in the tries as he extended the score to 31-0 courtesy of Owen Farrell’s conversion.
Nowell, Tom Curry and Joe Launchbury were the scorers of the earlier touchdowns.
Scotland were able to pull one back before half-time as hooker Stuart McInally ran 55 yards after charging Farrell’s attempted clearance.
England took a 31-7 advantage into the break which was greeted by cheers from the home faithful, who will have been disheartened from results earlier in the day.
Wales beat Ireland to win the Grand Slam and Six Nations title.
It rendered England’s clash with Scotland a dead rubber.
Wales had not won the Championship in five years but they scored inside the opening two minutes before easing to a 25-7 win.
England will finish second to Wales in the group, barring a catastrophic collapse in the second half.