A number of his players, including centre Ben Te’o, had played down the animosity between the two teams and insisted the rivalry would pale into insignificance.
However, when the two teams came off the field after their pre-match warm-ups, footage shows players from both sides grabbing each other’s jerseys as emotions boiled over in the tunnel.
The BBC reported that Owen Farrell had been at the forefront of the confrontation and Scotland captain John Barclay had played peacemaker.
And Jones refused to deny that anything had happened between the two teams and did not seem quick to admonish his players for engaging.
“I don’t know, I don’t think so, these things happen,” Jones said.
But the Australian coach, contemplating defeat with England for just the second time in more than two years, was quick to pay tribute to the performance of Scotland, whose 25-13 victory was their first in the Calcutta Cup since 2008.
“Scotland were too good and played some great rugby,” Jones added.
“They got a jump on us in the first half and we couldn’t get it back.
“They found holes in our defence and dominated the breakdown.
“It’s a great lesson. We have to improve our breakdown work, our spacing in defence and how to play with intensity right from the start.
“Human beings aren’t robots. We prepare to be intense and aggressive but for some reason we weren’t.”
And Jones was at a loss to explain why his team had been so sluggish in the first half, when they were outscored 22-6 and three tries to none.
“It’s human nature, unfortunately we just weren’t in the game for the first 40 minutes, so full marks to Scotland,” Jones said.
“We knew what we were going to get, but we just couldn’t meet the challenge today.
“We’ve got two games to go, and we’ll look to learn from what happened today, and put our best foot forward.”