It is thought the plastic bottle struck the head of England's high performance coach, Neil Craig.
The visitors won a towsy match 13-6 to reclaim the Calcutta Cup in terrible conditions in Edinburgh.
Jones, the England head coach, accused the Murrayfield crowd being "aggressive" and "without manners".
“We weren’t expecting beer bottles to be thrown at us,” he said. “That’s a new trick. It’s a pretty good achievement, isn’t it? Throwing beer bottles. You’ve got to be pretty brave to throw a beer bottle.”Asked if Craig was okay, Jones joked: “Well, he’s got a hard head, not much inside it.”Jones said he would not be making a complaint about the incident.“It’s not going to do anything, is it?” he said. “Everyone knows about it so someone can do something about it. Look, it’s not good behaviour, is it?”
Australian-born Craig, 64, has been England's head of high performance since 2017.
It is understood that the Scottish Rugby Union have offered the England management an apology for the alleged incident.